From c8fed0928e983c1f598e8563fe79f04e67d2f085 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Apr 2026 05:07:41 +0000
Subject: [PATCH 01/10] Add log_and_raise helper and convert duplicate
 fre_logger.error/raise patterns

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/98852929-27ab-48b1-8b84-1787a26e72f3

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/__init__.py                               | 19 +++++++
 .../generate_time_averages/cdoTimeAverager.py |  4 +-
 .../generate_time_averages.py                 |  5 +-
 fre/cmor/cmor_helpers.py                      | 24 ++++----
 fre/cmor/cmor_mixer.py                        |  6 +-
 fre/pp/configure_script_yaml.py               |  8 +--
 fre/pp/split_netcdf_script.py                 |  7 +--
 fre/tests/test_fre_log_and_raise.py           | 56 +++++++++++++++++++
 8 files changed, 103 insertions(+), 26 deletions(-)
 create mode 100644 fre/tests/test_fre_log_and_raise.py

diff --git a/fre/__init__.py b/fre/__init__.py
index 3a3702c89..50147a4b9 100644
--- a/fre/__init__.py
+++ b/fre/__init__.py
@@ -14,3 +14,22 @@
                     format = FORMAT,
                     filename = None,
                     encoding = 'utf-8' )
+
+
+def log_and_raise(msg, exc_type=ValueError, exc=None):
+    """
+    Log an error message via fre_logger and raise an exception with the same message.
+    Avoids the need to duplicate error text in both fre_logger.error() and raise calls.
+
+    :param msg: Error message to log and include in the exception.
+    :type msg: str
+    :param exc_type: Exception class to raise. Defaults to ValueError.
+    :type exc_type: type
+    :param exc: Optional original exception to chain from (uses ``raise ... from exc``).
+    :type exc: Exception, optional
+    :raises exc_type: Always raised with the given message.
+    """
+    fre_logger.error(msg, stacklevel=2)
+    if exc is not None:
+        raise exc_type(msg) from exc
+    raise exc_type(msg)
diff --git a/fre/app/generate_time_averages/cdoTimeAverager.py b/fre/app/generate_time_averages/cdoTimeAverager.py
index c8f585887..125fbf1f3 100644
--- a/fre/app/generate_time_averages/cdoTimeAverager.py
+++ b/fre/app/generate_time_averages/cdoTimeAverager.py
@@ -8,6 +8,7 @@
 import cdo
 from cdo import Cdo
 
+from fre import log_and_raise
 from .timeAverager import timeAverager
 
 fre_logger = logging.getLogger(__name__)
@@ -32,8 +33,7 @@ def generate_timavg(self, infile = None, outfile = None):
         """
 
         if self.avg_type not in ['all', 'seas', 'month']:
-            fre_logger.error('requested unknown avg_type %s.', self.avg_type)
-            raise ValueError(f'requested unknown avg_type {self.avg_type}')
+            log_and_raise(f'requested unknown avg_type {self.avg_type}')
 
         if self.var is not None:
             fre_logger.warning('WARNING: variable specification not twr supported for cdo time averaging. ignoring!')
diff --git a/fre/app/generate_time_averages/generate_time_averages.py b/fre/app/generate_time_averages/generate_time_averages.py
index 2d0f0a874..470597741 100755
--- a/fre/app/generate_time_averages/generate_time_averages.py
+++ b/fre/app/generate_time_averages/generate_time_averages.py
@@ -11,6 +11,8 @@
 from .frenctoolsTimeAverager import frenctoolsTimeAverager
 from .frepytoolsTimeAverager import frepytoolsTimeAverager
 
+from fre import log_and_raise
+
 fre_logger = logging.getLogger(__name__)
 
 def generate_time_average(infile: Union[str, List[str]] = None,
@@ -98,8 +100,7 @@ def generate_time_average(infile: Union[str, List[str]] = None,
         exitstatus = myavger.generate_timavg( infile = infile,
                                               outfile = outfile)
     else:
-        fre_logger.error('averager is None, check generate_time_average in generate_time_averages.py!')
-        raise ValueError
+        log_and_raise('averager is None, check generate_time_average in generate_time_averages.py!')
 
     # remove the new merged file if we created it.
     if merged:
diff --git a/fre/cmor/cmor_helpers.py b/fre/cmor/cmor_helpers.py
index a7e6c9033..aa3f35d9a 100644
--- a/fre/cmor/cmor_helpers.py
+++ b/fre/cmor/cmor_helpers.py
@@ -56,6 +56,8 @@
 from .cmor_constants import ( ARCHIVE_GOLD_DATA_DIR, CMIP7_GOLD_OCEAN_FILE_STUB, CMIP6_GOLD_OCEAN_FILE_STUB,
                               INPUT_TO_MIP_VERT_DIM )
 
+from fre import log_and_raise
+
 fre_logger = logging.getLogger(__name__)
 
 
@@ -457,10 +459,9 @@ def update_grid_and_label( json_file_path: str,
     .. note:: The function logs before and after values, and overwrites the input file unless an output path is given.
     """
     if None in [new_grid_label, new_grid, new_nom_res]:
-        fre_logger.error(
+        log_and_raise(
             'grid/grid_label/nom_res updating requested for exp_config file, but one of them is None\n'
             'bailing...!')
-        raise ValueError
 
     try:
         with open(json_file_path, "r", encoding="utf-8") as file:
@@ -471,24 +472,24 @@ def update_grid_and_label( json_file_path: str,
             data["grid"] = new_grid
             fre_logger.info('Updated "grid": %s', data["grid"])
         except KeyError as e:
-            fre_logger.error("Failed to update 'grid': %s", e)
-            raise KeyError("Error while updating 'grid'. Ensure the field exists and is modifiable.") from e
+            log_and_raise("Error while updating 'grid'. Ensure the field exists and is modifiable.",
+                          KeyError, exc=e)
 
         try:
             fre_logger.info('Original "grid_label": %s', data["grid_label"])
             data["grid_label"] = new_grid_label
             fre_logger.info('Updated "grid_label": %s', data["grid_label"])
         except KeyError as e:
-            fre_logger.error("Failed to update 'grid_label': %s", e)
-            raise KeyError("Error while updating 'grid_label'. Ensure the field exists and is modifiable.") from e
+            log_and_raise("Error while updating 'grid_label'. Ensure the field exists and is modifiable.",
+                          KeyError, exc=e)
 
         try:
             fre_logger.info('Original "nominal_resolution": %s', data["nominal_resolution"])
             data["nominal_resolution"] = new_nom_res
             fre_logger.info('Updated "nominal_resolution": %s', data["nominal_resolution"])
         except KeyError as e:
-            fre_logger.error("Failed to update 'nominal_resolution': %s", e)
-            raise KeyError("Error updating 'nominal_resolution'. Ensure the field exists and is modifiable.") from e
+            log_and_raise("Error updating 'nominal_resolution'. Ensure the field exists and is modifiable.",
+                          KeyError, exc=e)
 
         output_file_path = output_file_path or json_file_path
 
@@ -530,10 +531,9 @@ def update_calendar_type( json_file_path: str,
     .. note:: The function logs before and after values, and overwrites the input file unless an output path is given.
     """
     if new_calendar_type is None:
-        fre_logger.error(
+        log_and_raise(
             'calendar_type updating requested for exp_config file, but one of them is None\n'
             'bailing...!')
-        raise ValueError
 
     try:
         with open(json_file_path, "r", encoding="utf-8") as file:
@@ -544,8 +544,8 @@ def update_calendar_type( json_file_path: str,
             data["calendar"] = new_calendar_type
             fre_logger.info('Updated "calendar": %s', data["calendar"])
         except KeyError as e:
-            fre_logger.error("Failed to update 'calendar': %s", e)
-            raise KeyError("Error while updating 'calendar'. Ensure the field exists and is modifiable.") from e
+            log_and_raise("Error while updating 'calendar'. Ensure the field exists and is modifiable.",
+                          KeyError, exc=e)
 
         output_file_path = output_file_path or json_file_path
 
diff --git a/fre/cmor/cmor_mixer.py b/fre/cmor/cmor_mixer.py
index 43aa55d66..3e1513ff6 100755
--- a/fre/cmor/cmor_mixer.py
+++ b/fre/cmor/cmor_mixer.py
@@ -50,6 +50,8 @@
                               DEPTH_COORDS, CMOR_NC_FILE_ACTION, CMOR_VERBOSITY,
                               CMOR_EXIT_CTL, CMOR_MK_SUBDIRS, CMOR_LOG )
 
+from fre import log_and_raise
+
 fre_logger = logging.getLogger(__name__)
 
 def rewrite_netcdf_file_var( mip_var_cfgs: dict = None,
@@ -523,8 +525,8 @@ def rewrite_netcdf_file_var( mip_var_cfgs: dict = None,
                 lev_bnds = create_lev_bnds(bound_these=lev, with_these=ds['z_i'])
                 fre_logger.info('created lev_bnds...')
             except Exception as exc:
-                fre_logger.error("the cmor module always requires vertical levels to have bounds.")
-                raise KeyError("CMOR requires the input data have vertical level boundaries (bnds)") from exc
+                log_and_raise("CMOR requires the input data have vertical level boundaries (bnds)",
+                              KeyError, exc=exc)
 
             fre_logger.info('lev_bnds = \n%s', lev_bnds)
             cmor_z = cmor.axis('depth_coord',
diff --git a/fre/pp/configure_script_yaml.py b/fre/pp/configure_script_yaml.py
index a6fec203b..86538104d 100644
--- a/fre/pp/configure_script_yaml.py
+++ b/fre/pp/configure_script_yaml.py
@@ -13,6 +13,8 @@
 
 import fre.yamltools.combine_yamls_script as cy
 
+from fre import log_and_raise
+
 fre_logger = logging.getLogger(__name__)
 
 ######VALIDATE#####
@@ -127,8 +129,7 @@ def set_rose_suite(yamlfile: dict, rose_suite: metomi.rose.config.ConfigNode) ->
     pa_scripts = ""
     rd_scripts = ""
     if pp is None:
-        fre_logger.error("Missing 'postprocess' section!")
-        raise ValueError
+        log_and_raise("Missing 'postprocess' section!")
 
     for pp_key, pp_value in pp.items():
         if pp_key == "settings" or pp_key == "switches":
@@ -152,8 +153,7 @@ def set_rose_suite(yamlfile: dict, rose_suite: metomi.rose.config.ConfigNode) ->
                     # If there is already a script defined for preanalysis, fail
                     # More than 1 script is not supported yet
                     if pa_scripts:
-                        fre_logger.error("Using more than 1 pre-analysis script is not supported")
-                        raise ValueError
+                        log_and_raise("Using more than 1 pre-analysis script is not supported")
 
                     pa_scripts += f"{script} "
 
diff --git a/fre/pp/split_netcdf_script.py b/fre/pp/split_netcdf_script.py
index ed08688d6..fed7db58e 100644
--- a/fre/pp/split_netcdf_script.py
+++ b/fre/pp/split_netcdf_script.py
@@ -19,6 +19,7 @@
 import xarray as xr
 import yaml
 
+from fre import log_and_raise
 from fre.app.helpers import get_variables
 
 
@@ -66,8 +67,7 @@ def split_netcdf(inputDir, outputDir, component, history_source, use_subdirs,
 
     #Verify input/output dirs exist and are dirs
     if not os.path.isdir(inputDir):
-        fre_logger.error(f"error: input dir {inputDir} does not exist or is not a directory")
-        raise OSError(f"error: input dir {inputDir} does not exist or is not a directory")
+        log_and_raise(f"error: input dir {inputDir} does not exist or is not a directory", OSError)
     if not os.path.isdir(outputDir):
         if os.path.isfile(outputDir):
             fre_logger.error(f"error: output dir {outputDir} is a file. Please specify a directory.")
@@ -180,8 +180,7 @@ def split_file_xarray(infile, outfiledir, var_list='all'):
         os.makedirs(outfiledir)
 
     if not os.path.isfile(infile):
-        fre_logger.error(f"error: input file {infile} not found. Please check the path.")
-        raise OSError(f"error: input file {infile} not found. Please check the path.")
+        log_and_raise(f"error: input file {infile} not found. Please check the path.", OSError)
 
     dataset = xr.load_dataset(infile, decode_cf=False, decode_times=False, decode_coords="all")
     allvars = dataset.data_vars.keys()
diff --git a/fre/tests/test_fre_log_and_raise.py b/fre/tests/test_fre_log_and_raise.py
new file mode 100644
index 000000000..a08728bc1
--- /dev/null
+++ b/fre/tests/test_fre_log_and_raise.py
@@ -0,0 +1,56 @@
+"""
+Tests for the log_and_raise helper function in fre/__init__.py.
+
+Validates that log_and_raise:
+- logs an error message via fre_logger
+- raises the correct exception type with the expected message
+- supports exception chaining via the exc parameter
+- defaults to ValueError when no exc_type is given
+- reports the correct caller in log output (not log_and_raise itself)
+"""
+
+import logging
+
+import pytest
+
+from fre import log_and_raise
+
+
+def test_log_and_raise_default_valueerror(caplog):
+    ''' log_and_raise with default exc_type should raise ValueError and log an error '''
+    with caplog.at_level(logging.ERROR):
+        with pytest.raises(ValueError, match="something went wrong"):
+            log_and_raise("something went wrong")
+    assert "something went wrong" in caplog.text
+
+
+def test_log_and_raise_custom_exception_type(caplog):
+    ''' log_and_raise with custom exc_type should raise that type '''
+    with caplog.at_level(logging.ERROR):
+        with pytest.raises(OSError, match="file not found"):
+            log_and_raise("file not found", OSError)
+    assert "file not found" in caplog.text
+
+
+def test_log_and_raise_with_chained_exception(caplog):
+    ''' log_and_raise with exc should chain exceptions via from '''
+    original = KeyError("original key error")
+    with caplog.at_level(logging.ERROR):
+        with pytest.raises(KeyError, match="wrapped error") as exc_info:
+            log_and_raise("wrapped error", KeyError, exc=original)
+    assert exc_info.value.__cause__ is original
+    assert "wrapped error" in caplog.text
+
+
+def test_log_and_raise_caller_in_log(caplog):
+    ''' log output should reference the calling function, not log_and_raise '''
+    with caplog.at_level(logging.ERROR):
+        with pytest.raises(ValueError):
+            log_and_raise("test caller context")
+    # the log record funcName should be this test function, not 'log_and_raise'
+    for record in caplog.records:
+        if "test caller context" in record.message:
+            assert record.funcName == "test_log_and_raise_caller_in_log"
+            break
+    else:
+        pytest.fail("expected log record not found")

From 7bc513d6fcac0812d9c7a587b52170387a0f18a1 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Apr 2026 05:09:38 +0000
Subject: [PATCH 02/10] Address code review: add usage examples to
 log_and_raise docstring

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/98852929-27ab-48b1-8b84-1787a26e72f3

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/__init__.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/fre/__init__.py b/fre/__init__.py
index 50147a4b9..9b568a244 100644
--- a/fre/__init__.py
+++ b/fre/__init__.py
@@ -28,6 +28,18 @@ def log_and_raise(msg, exc_type=ValueError, exc=None):
     :param exc: Optional original exception to chain from (uses ``raise ... from exc``).
     :type exc: Exception, optional
     :raises exc_type: Always raised with the given message.
+
+    Examples::
+
+        # raises ValueError (default) and logs the message at ERROR level
+        log_and_raise("something went wrong")
+
+        # raises a specific exception type
+        log_and_raise("file not found", OSError)
+
+        # chains from an original exception (raise ... from exc)
+        except KeyError as e:
+            log_and_raise("update failed", KeyError, exc=e)
     """
     fre_logger.error(msg, stacklevel=2)
     if exc is not None:

From c3663414fa4ab442e0cf6b2b792368aa7b693352 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Apr 2026 05:47:08 +0000
Subject: [PATCH 03/10] Convert raise statements to log_and_raise across 33
 files

Replace bare raise ExcType(msg) statements with log_and_raise(msg, ExcType)
calls, which logs the error before raising. This ensures all raised exceptions
are consistently logged via fre_logger.error.

Changes:
- Add 'from fre import log_and_raise' imports where missing
- Convert raise ValueError/TypeError/FileNotFoundError/FileExistsError/
  IOError/RuntimeError/OSError/Exception/NotImplementedError/KeyError/
  NameError to log_and_raise equivalents
- For 'raise ExcType(msg) from exc' patterns, use log_and_raise(msg, ExcType, exc=exc)
- For patterns where fre_logger.error + raise had the same message, collapse
  into single log_and_raise call
- For patterns where fre_logger.error + raise had different messages, keep
  fre_logger.error and replace raise with log_and_raise
- Preserve all bare re-raises (raise with no arguments)
- Preserve NotImplementedError in abstract methods in timeAverager.py
- Collapse multi-line raise statements into single log_and_raise calls
- Convert multi-argument ValueError to single string message log_and_raise calls

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/app/generate_time_averages/combine.py     | 12 ++++-----
 .../frenctoolsTimeAverager.py                 | 11 ++++----
 .../generate_time_averages.py                 |  4 +--
 fre/app/generate_time_averages/wrapper.py     |  9 ++++---
 fre/app/helpers.py                            |  6 +++--
 .../mask_atmos_plevel/mask_atmos_plevel.py    |  8 +++---
 fre/app/regrid_xy/regrid_xy.py                | 14 +++++------
 .../remap_pp_components.py                    | 25 +++++++++----------
 fre/check/frecheck.py                         |  3 ++-
 fre/cmor/cmor_helpers.py                      |  4 +--
 fre/cmor/cmor_mixer.py                        |  5 ++--
 fre/cmor/cmor_yamler.py                       | 11 ++++----
 fre/make/create_checkout_script.py            | 10 +++++---
 fre/make/create_compile_script.py             |  3 ++-
 fre/make/create_docker_script.py              |  3 ++-
 fre/make/create_makefile_script.py            |  3 ++-
 fre/make/gfdlfremake/platformfre.py           | 21 ++++++++--------
 fre/make/gfdlfremake/targetfre.py             |  8 +++---
 fre/make/gfdlfremake/yamlfre.py               |  5 ++--
 fre/make/make_helpers.py                      |  4 ++-
 fre/make/run_fremake_script.py                |  3 ++-
 fre/pp/checkout_script.py                     |  9 ++++---
 fre/pp/histval_script.py                      |  7 +++---
 fre/pp/install_script.py                      |  3 ++-
 fre/pp/nccheck_script.py                      |  9 +++----
 fre/pp/ppval_script.py                        | 11 ++++----
 fre/pp/rename_split_script.py                 | 20 ++++++++-------
 fre/pp/run_script.py                          |  5 ++--
 fre/pp/split_netcdf_script.py                 | 19 ++++++--------
 fre/pp/status_script.py                       |  5 ++--
 fre/pp/trigger_script.py                      |  3 ++-
 fre/pp/validate_script.py                     |  7 +++---
 fre/run/frerun.py                             |  3 ++-
 33 files changed, 146 insertions(+), 127 deletions(-)

diff --git a/fre/app/generate_time_averages/combine.py b/fre/app/generate_time_averages/combine.py
index db8ffbc92..c96c34812 100644
--- a/fre/app/generate_time_averages/combine.py
+++ b/fre/app/generate_time_averages/combine.py
@@ -11,6 +11,7 @@
 import xarray as xr
 
 from ..helpers import change_directory
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 duration_parser = metomi.isodatetime.parsers.DurationParser()
@@ -35,8 +36,7 @@ def form_bronx_directory_name(frequency: str,
     elif frequency == "yr":
         frequency_label = "annual"
     else:
-        raise ValueError(f"Frequency '{frequency}' not recognized or supported")
-    interval_object = duration_parser.parse(interval)
+        log_and_raise(f"Frequency '{frequency}' not recognized or supported")
     return frequency_label + '_' + str(interval_object.years) + 'yr'
 
 
@@ -57,9 +57,9 @@ def merge_netcdfs(input_file_glob: str, output_file: str) -> None:
     if len(input_files) >= 1:
         fre_logger.debug(f"Input file search string '{input_file_glob}' matched {len(input_files)} files")
     else:
-        raise FileNotFoundError(f"'{input_file_glob}' resolves to no files")
+        log_and_raise(f"'{input_file_glob}' resolves to no files", FileNotFoundError)
     if Path(output_file).exists():
-        raise FileExistsError(f"Output file '{output_file}' already exists")
+        log_and_raise(f"Output file '{output_file}' already exists", FileExistsError)
 
     ds = xr.open_mfdataset(input_files, compat='override', coords='minimal')
     ds.to_netcdf(output_file, unlimited_dims=['time'])
@@ -93,9 +93,7 @@ def combine( root_in_dir: str,
     :rtype: None
     """
     if frequency not in ["yr", "mon"]:
-        raise ValueError(f"Frequency '{frequency}' not recognized or supported")
-
-    if frequency == "yr":
+        log_and_raise(f"Frequency '{frequency}' not recognized or supported")
         frequency_iso = "P1Y"
     elif frequency == "mon":
         frequency_iso = "P1M"
diff --git a/fre/app/generate_time_averages/frenctoolsTimeAverager.py b/fre/app/generate_time_averages/frenctoolsTimeAverager.py
index 59ebf95ce..00b05cc36 100644
--- a/fre/app/generate_time_averages/frenctoolsTimeAverager.py
+++ b/fre/app/generate_time_averages/frenctoolsTimeAverager.py
@@ -7,6 +7,7 @@
 
 from cdo import Cdo
 from .timeAverager import timeAverager
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -35,7 +36,7 @@ def generate_timavg(self, infile=None, outfile=None):
         """
         exitstatus=1
         if self.avg_type not in ['month','all']:
-            raise ValueError(f'avg_type= {self.avg_type} not supported by this class at this time.')
+            log_and_raise(f'avg_type= {self.avg_type} not supported by this class at this time.')
 
         if self.unwgt:
             fre_logger.warning('unwgt=True unsupported by frenctoolsAverager. Ignoring!!!')
@@ -45,7 +46,7 @@ def generate_timavg(self, infile=None, outfile=None):
                    ' not currently supported for frenctols time averaging. ignoring!', self.var)
 
         if infile is None:
-            raise ValueError('Need an input file, specify a value for the infile argument')
+            log_and_raise('Need an input file, specify a value for the infile argument')
 
         if outfile is None:
             outfile='frenctoolsTimeAverage_'+infile
@@ -53,7 +54,7 @@ def generate_timavg(self, infile=None, outfile=None):
 
         #check for existence of timavg.csh. If not found, issue might be that user is not in env with frenctools.
         if shutil.which('timavg.csh') is None:
-            raise ValueError('did not find timavg.csh')
+            log_and_raise('did not find timavg.csh')
         fre_logger.info('timeaverager using: %s', shutil.which("timavg.csh"))
 
 
@@ -106,7 +107,7 @@ def generate_timavg(self, infile=None, outfile=None):
 
                     if subp.returncode != 0:
                         fre_logger.error('stderror = %s', stderror)
-                        raise ValueError(f'error: timavg.csh had a problem, subp.returncode = {subp.returncode}')
+                        log_and_raise(f'error: timavg.csh had a problem, subp.returncode = {subp.returncode}')
 
                     fre_logger.info('%s climatology successfully ran',nc_monthly_file)
                     exitstatus=0
@@ -130,7 +131,7 @@ def generate_timavg(self, infile=None, outfile=None):
 
             if subp.returncode != 0:
                 fre_logger.error('stderror  = %s', stderror)
-                raise ValueError(f'error: timavgcsh command not properly executed, subp.returncode = {subp.returncode}')
+                log_and_raise(f'error: timavgcsh command not properly executed, subp.returncode = {subp.returncode}')
 
             fre_logger.info('climatology successfully ran')
             exitstatus = 0
diff --git a/fre/app/generate_time_averages/generate_time_averages.py b/fre/app/generate_time_averages/generate_time_averages.py
index 470597741..196fb0a47 100755
--- a/fre/app/generate_time_averages/generate_time_averages.py
+++ b/fre/app/generate_time_averages/generate_time_averages.py
@@ -42,9 +42,9 @@ def generate_time_average(infile: Union[str, List[str]] = None,
     start_time = time.perf_counter()
     fre_logger.debug('called generate_time_average')
     if None in [infile, outfile, pkg]:
-        raise ValueError('infile, outfile, and pkg are required inputs')
+        log_and_raise('infile, outfile, and pkg are required inputs')
     if pkg not in ['cdo', 'fre-nctools', 'fre-python-tools']:
-        raise ValueError(f'argument pkg = {pkg} not known, must be one of: cdo, fre-nctools, fre-python-tools')
+        log_and_raise(f'argument pkg = {pkg} not known, must be one of: cdo, fre-nctools, fre-python-tools')
     exitstatus = 1
     myavger = None
 
diff --git a/fre/app/generate_time_averages/wrapper.py b/fre/app/generate_time_averages/wrapper.py
index 661363327..2609be7e5 100644
--- a/fre/app/generate_time_averages/wrapper.py
+++ b/fre/app/generate_time_averages/wrapper.py
@@ -8,6 +8,7 @@
 from metomi.isodatetime.dumpers import TimePointDumper
 
 from . import generate_time_averages
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 one_year = DurationParser().parse('P1Y')
@@ -77,7 +78,7 @@ def generate_wrapper(cycle_point: str,
     input_interval = DurationParser().parse(input_interval)
 
     if frequency not in ["yr", "mon"]:
-        raise ValueError(f"Frequency '{frequency}' not recognized or supported")
+        log_and_raise(f"Frequency '{frequency}' not recognized or supported")
 
     # convert frequency 'yr' or 'mon' to ISO8601
     if frequency == 'mon':
@@ -109,7 +110,7 @@ def generate_wrapper(cycle_point: str,
                         fre_logger.debug("Annual ts to annual climo from source %s:%s variables",
                                          source, len(variables))
                     else:
-                        raise FileNotFoundError(f"Expected files not found in {subdir_yr}")
+                        log_and_raise(f"Expected files not found in {subdir_yr}", FileNotFoundError)
                 elif subdir_mon.exists():
                     results = glob.glob(str(subdir_mon / f"{source}.{yyyy}01-{zzzz}12.*.nc"))
                     if results:
@@ -118,7 +119,7 @@ def generate_wrapper(cycle_point: str,
                         fre_logger.debug("monthly ts to annual climo from source %s:%s variables",
                                          source, len(variables))
                     else:
-                        raise FileNotFoundError(f"Expected files not found in {subdir_mon}")
+                        log_and_raise(f"Expected files not found in {subdir_mon}", FileNotFoundError)
                 else:
                     fre_logger.debug('Skipping %s as it does not appear to be monthly or annual frequency', source)
                     fre_logger.debug('neither %s nor %s  exists', subdir_mon, subdir_yr)
@@ -132,7 +133,7 @@ def generate_wrapper(cycle_point: str,
                         fre_logger.debug("monthly ts to monthly climo from source %s:%s variables",
                                          source, len(variables))
                     else:
-                        raise FileNotFoundError(f"Expected files not found in {subdir}")
+                        log_and_raise(f"Expected files not found in {subdir}", FileNotFoundError)
                 else:
                     fre_logger.debug("Skipping %s as it does not appear to be monthly frequency", source)
                     fre_logger.debug(" %s does not exist", subdir)
diff --git a/fre/app/helpers.py b/fre/app/helpers.py
index 5548e3619..5f878d685 100644
--- a/fre/app/helpers.py
+++ b/fre/app/helpers.py
@@ -6,6 +6,8 @@
 
 import yaml
 
+from fre import log_and_raise
+
 
 fre_logger = logging.getLogger(__name__)
 
@@ -25,7 +27,7 @@ def get_variables(yml: dict, pp_comp: str) -> dict:
     fre_logger.debug(f"Yaml file information: {yml}")
     fre_logger.debug(f"PP component: {pp_comp}")
     if not isinstance(yml, dict):
-        raise TypeError("yml should be of type dict, but was of type " + str(type(yml)))
+        log_and_raise("yml should be of type dict, but was of type " + str(type(yml)), TypeError)
 
     src_vars={}
 
@@ -61,7 +63,7 @@ def get_variables(yml: dict, pp_comp: str) -> dict:
     # If the dictionary is empty (no overlap of pp components and components
     # in pp yaml) --> error
     if not src_vars:
-        raise ValueError(f"PP component, {pp_comp}, not found in pp yaml configuration!")
+        log_and_raise(f"PP component, {pp_comp}, not found in pp yaml configuration!")
 
     return src_vars
 
diff --git a/fre/app/mask_atmos_plevel/mask_atmos_plevel.py b/fre/app/mask_atmos_plevel/mask_atmos_plevel.py
index 65c3a7f79..9f47a0f91 100755
--- a/fre/app/mask_atmos_plevel/mask_atmos_plevel.py
+++ b/fre/app/mask_atmos_plevel/mask_atmos_plevel.py
@@ -8,6 +8,8 @@
 
 import xarray as xr
 
+from fre import log_and_raise
+
 fre_logger = logging.getLogger(__name__)
 
 
@@ -42,7 +44,7 @@ def mask_atmos_plevel_subtool(infile: str = None,
     """
     # check if input file exists, raise an error if not
     if not os.path.exists(infile):
-        raise FileNotFoundError(f"ERROR: Input file {infile} does not exist")
+        log_and_raise(f"ERROR: Input file {infile} does not exist", FileNotFoundError)
 
     # Warn if outfile exists, but continue and recreate
     if os.path.exists(outfile):
@@ -62,7 +64,7 @@ def mask_atmos_plevel_subtool(infile: str = None,
     if "ps" not in list(ds_ps.variables):
         fre_logger.warning('pressure variable ps not found in target pressure file')
         if not warn_no_ps:
-            raise ValueError(f"Surface pressure file {psfile} does not contain surface pressure.")
+            log_and_raise(f"Surface pressure file {psfile} does not contain surface pressure.")
         fre_logger.warning('warn_no_ps is True! this means I\'m going to no-op gracefully instead of raising an error')
         return
 
@@ -143,7 +145,7 @@ def mask_field_above_surface_pressure(ds: xr.Dataset,
     try:
         missing_value = ds[var].encoding['missing_value']
     except Exception as exc:
-        raise KeyError("input file does not contain missing_value, a required variable attribute") from exc
+        log_and_raise("input file does not contain missing_value, a required variable attribute", KeyError, exc=exc)
 
     fre_logger.info('masking do not need looping')
     masked = xr.where(plev_extended > ps_extended, missing_value, ds[var])
diff --git a/fre/app/regrid_xy/regrid_xy.py b/fre/app/regrid_xy/regrid_xy.py
index f70d6e472..3f2533061 100644
--- a/fre/app/regrid_xy/regrid_xy.py
+++ b/fre/app/regrid_xy/regrid_xy.py
@@ -7,6 +7,7 @@
 import yaml
 
 from fre.app import helpers
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -83,7 +84,7 @@ def get_grid_spec(datadict: dict) -> str:
     elif Path("grid_spec.nc").exists():
         grid_spec = "grid_spec.nc"
     else:
-        raise IOError(f"Cannot find mosaic.nc or grid_spec.nc in tar file {pp_grid_spec_tar}")
+        log_and_raise(f"Cannot find mosaic.nc or grid_spec.nc in tar file {pp_grid_spec_tar}", IOError)
 
     fre_logger.debug(f"Current directory: {Path.cwd()}")
 
@@ -122,7 +123,7 @@ def get_input_mosaic(datadict: dict) -> str:
 
     #check if the mosaic file exists in the current directory
     if not Path(mosaic_file).exists():
-        raise IOError(f"Cannot find mosaic file {mosaic_file} in current work directory {work_dir}")
+        log_and_raise(f"Cannot find mosaic file {mosaic_file} in current work directory {work_dir}", IOError)
 
     return mosaic_file
 
@@ -299,16 +300,15 @@ def regrid_xy(yamlfile: str,
 
     #check if input_dir exists
     if not Path(input_dir).exists():
-        raise RuntimeError(f"Input directory {input_dir} containing the input data files does not exist")
+        log_and_raise(f"Input directory {input_dir} containing the input data files does not exist", RuntimeError)
 
     #check if output_dir exists
     if not Path(output_dir).exists():
-        raise RuntimeError(f"Output directory {output_dir} where regridded data" \
-                            "will be outputted does not exist")
+        log_and_raise(f"Output directory {output_dir} where regridded data will be outputted does not exist", RuntimeError)
 
     #check if work_dir exists
     if not Path(work_dir).exists():
-        raise RuntimeError(f"Specified working directory {work_dir} does not exist")
+        log_and_raise(f"Specified working directory {work_dir} does not exist", RuntimeError)
 
     #work in working directory
     with helpers.change_directory(work_dir):
@@ -399,4 +399,4 @@ def regrid_xy(yamlfile: str,
             if fregrid_job.returncode == 0:
                 fre_logger.info(fregrid_job.stdout.split("\n")[-3:])
             else:
-                raise RuntimeError(fregrid_job.stderr)
+                log_and_raise(fregrid_job.stderr, RuntimeError)
diff --git a/fre/app/remap_pp_components/remap_pp_components.py b/fre/app/remap_pp_components/remap_pp_components.py
index 5bcdc924c..2a74fc93d 100755
--- a/fre/app/remap_pp_components/remap_pp_components.py
+++ b/fre/app/remap_pp_components/remap_pp_components.py
@@ -11,6 +11,7 @@
 from typing import List
 import yaml
 from fre.app import helpers
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -32,13 +33,13 @@ def verify_dirs(in_dir: str, out_dir: str):
     if Path(in_dir).is_dir():
         fre_logger.info("Input directory is a valid directory")
     else:
-        raise ValueError(f"Error: Input directory {in_dir} does not exist or is not a valid directory")
+        log_and_raise(f"Error: Input directory {in_dir} does not exist or is not a valid directory")
 
     # Verify output directory exists and is a directory
     if Path(out_dir).is_dir():
         fre_logger.info("Output directory is a valid directory")
     else:
-        raise ValueError(f"Error: Output directory {out_dir} does not exist or is not a valid directory")
+        log_and_raise(f"Error: Output directory {out_dir} does not exist or is not a valid directory")
 
 def create_dir(out_dir: str, comp: str, freq: str, chunk:str, ens:str, dir_ts: bool) -> str:
     """
@@ -115,7 +116,7 @@ def freq_to_legacy(iso_dura: str) -> str:
     elif iso_dura in ['PT30M', 'PT0.5H']:
         freq_legacy = '30min'
     else:
-        raise ValueError(f"Could not convert ISO duration '{iso_dura}'")
+        log_and_raise(f"Could not convert ISO duration '{iso_dura}'")
 
     return freq_legacy
 
@@ -161,7 +162,7 @@ def freq_to_date_format(iso_freq: str) -> str:
     elif (iso_freq[:2]=='PT') and (iso_freq[-1:]=='H'):
         return 'CCYYMMDDThh'
     else:
-        raise ValueError(f'ERROR: Unknown Frequency {iso_freq}')
+        log_and_raise(f'ERROR: Unknown Frequency {iso_freq}')
 
 def truncate_date(date: str, freq: str) -> str:
     """
@@ -231,7 +232,7 @@ def search_files(product: str, var: list, source: str, freq: str,
                 fre_logger.info("var: %s", v)
                 f = glob.glob(f"{source}.{v}*.nc")
                 if not f: #if glob returns empty list
-                    raise ValueError("Variable {v} could not be found or does not exist.")
+                    log_and_raise("Variable {v} could not be found or does not exist.")
                 files.extend(f)
     else:
         if product == "ts":
@@ -240,7 +241,7 @@ def search_files(product: str, var: list, source: str, freq: str,
         elif product == "av":
             date = truncate_date(begin, "P1Y")
         else:
-            raise ValueError("Product not set to ts or av.")
+            log_and_raise("Product not set to ts or av.")
 
         if var == "all":
             f = glob.glob(f"{source}.{date}-*.*.nc")
@@ -250,7 +251,7 @@ def search_files(product: str, var: list, source: str, freq: str,
                 fre_logger.info("var: %s", v)
                 f = glob.glob(f"{source}.{date}-*.{v}*.nc")
                 if not f: #if glob returns empty list
-                    raise ValueError("Variable {v} could not be found or does not exist.")
+                    log_and_raise("Variable {v} could not be found or does not exist.")
                 files.extend(f)
         if product == "av" and current_chunk == "P1Y":
             f = glob.glob(f"{source}.{date}.*.nc")
@@ -276,7 +277,7 @@ def get_varlist(comp_info: dict, product: str, req_source: str, src_vars: dict)
     """
     if product == "static":
         if comp_info.get("static") is None:
-            raise ValueError(
+            log_and_raise(
                 f"Product is set to static but no static sources/variables defined for "
                 f"{comp_info.get('type')}"
             )
@@ -542,11 +543,9 @@ def remap_pp_components(input_dir: str, output_dir: str, begin_date: str, curren
 
                             if not files:
                                 if ens_mem is not None:
-                                    raise ValueError("\nError: No input files found in",
-                                                     f"{input_dir}/{g}/{ens_mem}/{s}/{f}/{c}")
+                                    log_and_raise(f"\nError: No input files found in {input_dir}/{g}/{ens_mem}/{s}/{f}/{c}")
                                 else:
-                                    raise ValueError("\nError: No input files found in",
-                                                     f"{input_dir}/{g}/{s}/{f}/{c}")
+                                    log_and_raise(f"\nError: No input files found in {input_dir}/{g}/{s}/{f}/{c}")
 
                             os.chdir(output_dir)
 
@@ -592,7 +591,7 @@ def remap_pp_components(input_dir: str, output_dir: str, begin_date: str, curren
                             if offline_srcs is not None:
                                 for src_file in offline_srcs:
                                     if not Path(src_file).exists():
-                                        raise ValueError("Offline diagnostic file defined but "
+                                        log_and_raise("Offline diagnostic file defined but "
                                                          f"{src_file} does not exist or cannot "
                                                          "be found!")
 
diff --git a/fre/check/frecheck.py b/fre/check/frecheck.py
index 4c1cf4f4d..1fe0fb2ae 100644
--- a/fre/check/frecheck.py
+++ b/fre/check/frecheck.py
@@ -3,6 +3,7 @@
 import click
 
 from .frecheckexample import check_test_function
+from fre import log_and_raise
 
 @click.group(help=click.style(" - check subcommands !!!NotImplemented!!!", fg=(162,91,232)))
 def check_cli():
@@ -13,4 +14,4 @@ def check_cli():
 def function(uppercase):
     """ - Execute fre check test """
     check_test_function(uppercase)
-    raise NotImplementedError('fre check has not been implemented yet!')
+    log_and_raise('fre check has not been implemented yet!', NotImplementedError)
diff --git a/fre/cmor/cmor_helpers.py b/fre/cmor/cmor_helpers.py
index aa3f35d9a..f60425eb3 100644
--- a/fre/cmor/cmor_helpers.py
+++ b/fre/cmor/cmor_helpers.py
@@ -773,12 +773,12 @@ def filter_brands( brands: list,
     if len(filtered_brands) == 0:
         fre_logger.error('cmip7 brand disambiguation eliminated all candidates '
                          'from %s', brands)
-        raise ValueError(
+        log_and_raise(
             f'multiple brands {brands} found for {target_var}, '
             f'but none survived disambiguation filtering')
 
     fre_logger.error('cmip7 brand disambiguation could not resolve between '
                      '%s', filtered_brands)
-    raise ValueError(
+    log_and_raise(
         f'multiple brands {filtered_brands} remain for {target_var} after '
         f'disambiguation \u2014 cannot determine which brand to use')
diff --git a/fre/cmor/cmor_mixer.py b/fre/cmor/cmor_mixer.py
index 3e1513ff6..ae5d0611f 100755
--- a/fre/cmor/cmor_mixer.py
+++ b/fre/cmor/cmor_mixer.py
@@ -146,9 +146,8 @@ def rewrite_netcdf_file_var( mip_var_cfgs: dict = None,
                     input_vert_dim = get_vertical_dimension(ds, target_var)
                 )
         else:
-            fre_logger.error('cmip7 case detected, but dimensions of input data do not match '
-                             'any of those found for the associated brands.')
-            raise ValueError
+            log_and_raise('cmip7 case detected, but dimensions of input data do not match '
+                             'any of those found for the associated brands.', ValueError)
     else:
         fre_logger.debug('non-cmip7 case detected, skipping variable brands')
 
diff --git a/fre/cmor/cmor_yamler.py b/fre/cmor/cmor_yamler.py
index f1569a7bb..a4549dece 100644
--- a/fre/cmor/cmor_yamler.py
+++ b/fre/cmor/cmor_yamler.py
@@ -24,6 +24,7 @@
 from .cmor_mixer import cmor_run_subtool
 from .cmor_helpers import ( check_path_existence, iso_to_bronx_chunk, #conv_mip_to_bronx_freq,
                             get_bronx_freq_from_mip_table )
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -123,8 +124,8 @@ def cmor_yaml_subtool( yamlfile: str = None,
             fre_logger.info('attempt to create it...')
             Path(cmorized_outdir).mkdir(exist_ok=False, parents=True)
         except Exception as exc: #uncovered
-            raise OSError(
-                f'could not create cmorized_outdir = {cmorized_outdir} for some reason!') from exc
+            log_and_raise(
+                f'could not create cmorized_outdir = {cmorized_outdir} for some reason!', OSError, exc=exc)
 
     # path to input user/experiment configuration, expected by CMOR
     json_exp_config = os.path.expandvars(
@@ -179,7 +180,7 @@ def cmor_yaml_subtool( yamlfile: str = None,
         if freq is None:
             if mip_era == 'CMIP7':
                 # CMIP7 tables do not carry frequency — the user must always specify it
-                raise ValueError(
+                log_and_raise(
                     f'freq is required for CMIP7 but was not specified for table target {table_name}.\n'
                     f'  CMIP7 MIP tables do not contain frequency metadata.\n'
                     f'  please set freq explicitly (e.g. "monthly", "daily") in the cmor yaml.')
@@ -191,7 +192,7 @@ def cmor_yaml_subtool( yamlfile: str = None,
             except (KeyError, TypeError):
                 freq = None
             if freq is None:
-                raise ValueError(
+                log_and_raise(
                     f'not enough frequency information to process variables for {table_name}.\n'
                     f'  freq was not specified in the cmor yaml, and could not be derived from the MIP table.\n'
                     f'  please set freq explicitly (e.g. "monthly", "daily") in the cmor yaml.')
@@ -210,7 +211,7 @@ def cmor_yaml_subtool( yamlfile: str = None,
             grid_desc = gridding_dict['grid_desc']
             nom_res = gridding_dict['nom_res']
             if None in [grid_label, grid_desc, nom_res]:
-                raise ValueError('gridding dictionary, if present, must have all three fields be non-empty.')
+                log_and_raise('gridding dictionary, if present, must have all three fields be non-empty.')
         # gridding info of data ---- revisit
 
         table_components_list = cmor_yaml_table_target['target_components']
diff --git a/fre/make/create_checkout_script.py b/fre/make/create_checkout_script.py
index e2595abea..02ccf6126 100644
--- a/fre/make/create_checkout_script.py
+++ b/fre/make/create_checkout_script.py
@@ -18,6 +18,7 @@
 from typing import Optional
 import fre.yamltools.combine_yamls_script as cy
 from .gfdlfremake import varsfre, yamlfre, checkout, targetfre
+from fre import log_and_raise
 
 # set up logging
 fre_logger = logging.getLogger(__name__)
@@ -115,7 +116,7 @@ def checkout_create(yamlfile: str, platform: tuple, target: tuple,
     jobs_str = str(njobs)
 
     if isinstance(njobs, bool) and execute:
-        raise ValueError ('njobs must be defined as a number if --execute flag is True')
+        log_and_raise('njobs must be defined as a number if --execute flag is True')
 
     # Determine backgrounding syntax
     # parallel_cmd is the suffix added to shell commands
@@ -151,7 +152,7 @@ def checkout_create(yamlfile: str, platform: tuple, target: tuple,
 
     for platform_name in platform:
         if not model_yaml.platforms.hasPlatform(platform_name):
-            raise ValueError(f"{platform_name} does not exist in platforms.yaml")
+            log_and_raise(f"{platform_name} does not exist in platforms.yaml")
 
         platform_info = model_yaml.platforms.getPlatformFromName(platform_name)
 
@@ -180,8 +181,9 @@ def checkout_create(yamlfile: str, platform: tuple, target: tuple,
                     try:
                         subprocess.run(args=[checkout_sh_path], check=True)
                     except Exception as exc:
-                        raise OSError(f"\nError executing checkout script: {checkout_sh_path}.",
-                                      f"\nTry removing test folder: {platform_info['modelRoot']}\n") from exc
+                        log_and_raise(f"\nError executing checkout script: {checkout_sh_path}."
+                                       f"\nTry removing test folder: {platform_info['modelRoot']}\n",
+                                       OSError, exc=exc)
                 else:
                     return
 
diff --git a/fre/make/create_compile_script.py b/fre/make/create_compile_script.py
index b40cf228f..4a50964fd 100644
--- a/fre/make/create_compile_script.py
+++ b/fre/make/create_compile_script.py
@@ -31,6 +31,7 @@
     yamlfre
 )
 
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -101,7 +102,7 @@ def compile_create(yamlfile:str, platform:tuple[str], target:tuple[str], makejob
         for target_name in tlist:
             target = targetfre.fretarget(target_name)
             if not model_yaml.platforms.hasPlatform(platform_name):
-                raise ValueError(f"{platform_name} does not exist in platforms.yaml")
+                log_and_raise(f"{platform_name} does not exist in platforms.yaml")
 
             platform = model_yaml.platforms.getPlatformFromName(platform_name)
             ## Make the bld_dir based on the modelRoot, the platform, and the target
diff --git a/fre/make/create_docker_script.py b/fre/make/create_docker_script.py
index 84752b10d..70d670ec0 100644
--- a/fre/make/create_docker_script.py
+++ b/fre/make/create_docker_script.py
@@ -23,6 +23,7 @@
     yamlfre
 )
 
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -79,7 +80,7 @@ def dockerfile_create(yamlfile: str, platform: tuple[str], target: tuple[str],
         for targetName in tlist:
             targetObject = targetfre.fretarget(targetName)
             if not modelYaml.platforms.hasPlatform(platformName):
-                raise ValueError (f"{platformName} does not exist in platforms.yaml")
+                log_and_raise(f"{platformName} does not exist in platforms.yaml")
 
             platform = modelYaml.platforms.getPlatformFromName(platformName)
 
diff --git a/fre/make/create_makefile_script.py b/fre/make/create_makefile_script.py
index 896edb079..47bc96349 100644
--- a/fre/make/create_makefile_script.py
+++ b/fre/make/create_makefile_script.py
@@ -37,6 +37,7 @@
 import fre.yamltools.combine_yamls_script as cy
 from fre.make.make_helpers import get_mktemplate_path
 from .gfdlfremake import makefilefre, varsfre, targetfre, yamlfre
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -92,7 +93,7 @@ def makefile_create(yamlfile: str, platform: tuple[str], target: tuple[str]):
             if model_yaml.platforms.hasPlatform(platform_name):
                 pass
             else:
-                raise ValueError (f"{platform_name} does not exist in platforms.yaml")
+                log_and_raise(f"{platform_name} does not exist in platforms.yaml")
 
             platform=model_yaml.platforms.getPlatformFromName(platform_name)
             ## Make the bld_dir based on the modelRoot, the platform, and the target
diff --git a/fre/make/gfdlfremake/platformfre.py b/fre/make/gfdlfremake/platformfre.py
index 1d6b0f049..898404cdc 100644
--- a/fre/make/gfdlfremake/platformfre.py
+++ b/fre/make/gfdlfremake/platformfre.py
@@ -1,4 +1,5 @@
 import yaml
+from fre import log_and_raise
 
 class platforms ():
     def __init__(self,platforminfo):
@@ -17,12 +18,12 @@ def __init__(self,platforminfo):
             try:
                 p["name"]
             except:
-                raise Exception("At least one of the platforms is missing a name in "+fname+"\n")
+                log_and_raise("At least one of the platforms is missing a name in "+fname+"\n", Exception)
             ## Check the compiler
             try:
                 p["compiler"]
             except:
-                raise Exception("You must specify a compiler in your "+p["name"]+" platform in the file "+fname+"\n")
+                log_and_raise("You must specify a compiler in your "+p["name"]+" platform in the file "+fname+"\n", Exception)
             ## Check for list of commands that include modules to initialize, load, and unload
             try:
                 p["envSetup"]
@@ -52,14 +53,14 @@ def __init__(self,platforminfo):
                 try:
                     p["containerBuild"]
                 except:
-                    raise Exception("Platform "+p["name"]+": You must specify the program used to build the container (containerBuild) on the "+p["name"]+" platform in the file "+fname+"\n")
+                    log_and_raise("Platform "+p["name"]+": You must specify the program used to build the container (containerBuild) on the "+p["name"]+" platform in the file "+fname+"\n", Exception)
                 if p["containerBuild"] != "podman" and p["containerBuild"] != "docker":
-                    raise ValueError("Platform "+p["name"]+": Container builds only supported with docker or podman, but you listed "+p["containerBuild"]+"\n")
+                    log_and_raise("Platform "+p["name"]+": Container builds only supported with docker or podman, but you listed "+p["containerBuild"]+"\n")
                 ## Get the name of the base container
                 try:
                     p["containerBase"]
                 except:
-                    raise NameError("Platform "+p["name"]+": You must specify the base container you wish to use to build your application")
+                    log_and_raise("Platform "+p["name"]+": You must specify the base container you wish to use to build your application", NameError)
                 ## Check if this is a 2 step (multi stage) build
                 try:
                     p["container2step"]
@@ -70,7 +71,7 @@ def __init__(self,platforminfo):
                     try:
                         p["container2base"]
                     except:
-                        raise NameError ("Platform "+p["name"]+": container2step is True, so you must define a container2base\n")
+                        log_and_raise("Platform "+p["name"]+": container2step is True, so you must define a container2base\n", NameError)
                     ## Check if there is anything special to copy over
                 else:
                     ## There should not be a second base if this is not a 2 step build
@@ -79,7 +80,7 @@ def __init__(self,platforminfo):
                     except:
                         p["container2base"] = ""
                     else:
-                        raise ValueError ("Platform "+p["name"]+": You defined container2base "+p["container2base"]+" but container2step is False\n")
+                        log_and_raise("Platform "+p["name"]+": You defined container2base "+p["container2base"]+" but container2step is False\n")
                 ## Get any commands to execute in the dockerfile RUN command
                 try:
                     p["RUNenv"]
@@ -94,9 +95,9 @@ def __init__(self,platforminfo):
                 try:
                     p["containerRun"]
                 except:
-                    raise Exception("You must specify the program used to run the container (containerRun) on the "+p["name"]+" platform in the file "+fname+"\n")
+                    log_and_raise("You must specify the program used to run the container (containerRun) on the "+p["name"]+" platform in the file "+fname+"\n", Exception)
                 if p["containerRun"] != "apptainer" and p["containerRun"] != "singularity":
-                    raise ValueError("Container builds only supported with apptainer, but you listed "+p["containerRun"]+"\n")
+                    log_and_raise("Container builds only supported with apptainer, but you listed "+p["containerRun"]+"\n")
 
                 ## Get the path to where the output model container will be located
                 try:
@@ -108,7 +109,7 @@ def __init__(self,platforminfo):
                 try:
                     p["mkTemplate"]
                 except:
-                    raise ValueError("The platform "+p["name"]+" must specify a mkTemplate \n")
+                    log_and_raise("The platform "+p["name"]+" must specify a mkTemplate \n")
 
     def hasPlatform(self,name):
         """
diff --git a/fre/make/gfdlfremake/targetfre.py b/fre/make/gfdlfremake/targetfre.py
index e6fbfb1a6..4f5363228 100644
--- a/fre/make/gfdlfremake/targetfre.py
+++ b/fre/make/gfdlfremake/targetfre.py
@@ -1,3 +1,5 @@
+from fre import log_and_raise
+
 class fretarget:
     """
     Class: Stores information about the target
@@ -52,19 +54,19 @@ def __init__(self,t):
         if self.debug:
             try:
                 if self.repro or self.prod == True:
-                    raise ValueError(errormsg)
+                    log_and_raise(errormsg)
             except ValueError:
                 raise
         elif self.repro:
             try:
                 if self.prod == True:
-                    raise ValueError(errormsg)
+                    log_and_raise(errormsg)
             except ValueError:
                 raise
         else:
             try:
                 if self.prod == False:
-                    raise ValueError("Your target '"+self.target+"' needs to include one of the following: prod, repro, debug")
+                    log_and_raise("Your target '"+self.target+"' needs to include one of the following: prod, repro, debug")
             except ValueError:
                 raise
 
diff --git a/fre/make/gfdlfremake/yamlfre.py b/fre/make/gfdlfremake/yamlfre.py
index 50413c4d7..aca681deb 100644
--- a/fre/make/gfdlfremake/yamlfre.py
+++ b/fre/make/gfdlfremake/yamlfre.py
@@ -4,6 +4,7 @@
 import yaml
 from jsonschema import validate, ValidationError, SchemaError
 from . import platformfre
+from fre import log_and_raise
 
 def parseCompile(fname,v):
     """
@@ -32,12 +33,12 @@ def __init__(self,compileinfo):
         self.yaml = compileinfo
         # Check if self.yaml is None
         if self.yaml is None:
-            raise ValueError("The provided compileinfo is None. It must be a valid dictionary.")
+            log_and_raise("The provided compileinfo is None. It must be a valid dictionary.")
         ## Check for required experiment name
         try:
             self.yaml["experiment"]
         except KeyError:
-            raise KeyError("You must set an experiment name to compile \n")
+            log_and_raise("You must set an experiment name to compile \n", KeyError)
         ## Check for optional libraries and packages for linking in container
         try:
             self.yaml["container_addlibs"]
diff --git a/fre/make/make_helpers.py b/fre/make/make_helpers.py
index 243d66a39..c49d3c7ee 100644
--- a/fre/make/make_helpers.py
+++ b/fre/make/make_helpers.py
@@ -5,6 +5,8 @@
 import logging
 from pathlib import Path
 
+from fre import log_and_raise
+
 def get_mktemplate_path(mk_template: str, container_flag: bool, model_root: str = None) -> str:
 
     """
@@ -39,7 +41,7 @@ def get_mktemplate_path(mk_template: str, container_flag: bool, model_root: str
 
         # Check in template path exists
         if not Path(template_path).exists():
-            raise ValueError("Error w/ mkmf template. Created path from given "
+            log_and_raise("Error w/ mkmf template. Created path from given "
                              f"filename: {template_path} does not exist.")
     else:
         if "/" not in mk_template:
diff --git a/fre/make/run_fremake_script.py b/fre/make/run_fremake_script.py
index ec506cbc2..a11ac852c 100644
--- a/fre/make/run_fremake_script.py
+++ b/fre/make/run_fremake_script.py
@@ -13,6 +13,7 @@
 from fre.make.create_compile_script import compile_create
 from fre.make.create_docker_script import dockerfile_create
 from .gfdlfremake import (varsfre, yamlfre)
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -89,7 +90,7 @@ def fremake_run(yamlfile:str, platform:str, target:str,
     container_platforms = ()
     for platform_name in plist:
         if not model_yaml.platforms.hasPlatform(platform_name):
-            raise ValueError (f"{platform_name} does not exist in platforms.yaml")
+            log_and_raise(f"{platform_name} does not exist in platforms.yaml")
 
         platform_info = model_yaml.platforms.getPlatformFromName(platform_name)
 
diff --git a/fre/pp/checkout_script.py b/fre/pp/checkout_script.py
index 1c7c90849..8262feec0 100644
--- a/fre/pp/checkout_script.py
+++ b/fre/pp/checkout_script.py
@@ -11,6 +11,7 @@
 
 from . import make_workflow_name
 from ..fre import version as fre_ver
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -50,7 +51,7 @@ def checkout_template(experiment = None, platform = None, target = None, branch
     # check args + set the name of the directory
     if None in [experiment, platform, target]:
         os.chdir(go_back_here)
-        raise ValueError( 'one of these are None: experiment / platform / target = \n'
+        log_and_raise( 'one of these are None: experiment / platform / target = \n'
                          f'{experiment} / {platform} / {target}' )
     #name = f"{experiment}__{platform}__{target}"
     workflow_name = make_workflow_name(experiment, platform, target)
@@ -60,8 +61,8 @@ def checkout_template(experiment = None, platform = None, target = None, branch
     try:
         os.makedirs(directory, exist_ok = True)
     except Exception as exc:
-        raise OSError(
-            f"(checkoutScript) directory {directory} wasn't able to be created. exit!") from exc
+        log_and_raise(
+            f"(checkoutScript) directory {directory} wasn't able to be created. exit!", OSError, exc=exc)
     finally:
         os.chdir(go_back_here)
 
@@ -96,7 +97,7 @@ def checkout_template(experiment = None, platform = None, target = None, branch
             fre_logger.info(
                 f"ERROR: current branch is '{current_branch}', current tag-describe is '{current_tag}'")
             os.chdir(go_back_here)
-            raise ValueError('neither tag nor branch matches the git clone branch arg') #exit(1)
+            log_and_raise('neither tag nor branch matches the git clone branch arg')
 
     # make sure we are back where we should be
     if os.getcwd() != go_back_here:
diff --git a/fre/pp/histval_script.py b/fre/pp/histval_script.py
index c00b16134..1e4d26078 100644
--- a/fre/pp/histval_script.py
+++ b/fre/pp/histval_script.py
@@ -8,6 +8,7 @@
 import logging
 import yaml
 from . import nccheck_script as ncc
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -53,8 +54,8 @@ def validate(history: str, date_string: str, warn: bool):
     # Make sure we found atleast one diag_manifest
     if diag_count < 1:
         if not warn:
-            raise FileNotFoundError(
-                f" No diag_manifest files were found in {history}. History files cannot be validated.")
+            log_and_raise(
+                f" No diag_manifest files were found in {history}. History files cannot be validated.", FileNotFoundError)
         fre_logger.warning(
             f" Warning: No diag_manifest files were found in {history}. History files cannot be validated.")
         return 0
@@ -90,7 +91,7 @@ def validate(history: str, date_string: str, warn: bool):
     #Error Handling
     if len(mismatches)!=0:
         fre_logger.error("Unexpected number of timesteps found")
-        raise ValueError(
+        log_and_raise(
               "\n" + str(len(mismatches)) + 
               " file(s) contain(s) an unexpected number of timesteps:\n" + 
               "\n".join(mismatches))
diff --git a/fre/pp/install_script.py b/fre/pp/install_script.py
index e6561697f..0be9164a0 100644
--- a/fre/pp/install_script.py
+++ b/fre/pp/install_script.py
@@ -6,6 +6,7 @@
 from pathlib import Path
 
 from . import make_workflow_name
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -47,7 +48,7 @@ def install_subtool(experiment, platform, target):
         else:
             fre_logger.error(f"ERROR: Please remove installed workflow with 'cylc clean {workflow_name}'"
                   " or move the workflow run directory '{install_dir}'")
-            raise Exception(f"ERROR: Workflow '{install_dir}' already installed, and the definition has changed!")
+            log_and_raise(f"ERROR: Workflow '{install_dir}' already installed, and the definition has changed!", Exception)
     else:
         fre_logger.info(f"NOTE: About to install workflow into ~/cylc-run/{workflow_name}")
         cmd = f"cylc install --no-run-name {workflow_name}"
diff --git a/fre/pp/nccheck_script.py b/fre/pp/nccheck_script.py
index c00703126..985e77754 100644
--- a/fre/pp/nccheck_script.py
+++ b/fre/pp/nccheck_script.py
@@ -2,6 +2,8 @@
 import logging
 import netCDF4
 
+from fre import log_and_raise
+
 fre_logger = logging.getLogger(__name__)
 
 
@@ -37,12 +39,7 @@ def check(file_path: str, num_steps: int):
         return 0
 
     else:
-        fre_logger.error(
-            f" Unexpected number of timesteps found in {file_path}. "
-            f"Found: {num_actual_steps} timesteps  "
-            f"Expected: {num_steps} timesteps"
-        )
-        raise ValueError(
+        log_and_raise(
             f" Unexpected number of timesteps found in {file_path}. "
             f"Found: {num_actual_steps} timesteps  "
             f"Expected: {num_steps} timesteps"
diff --git a/fre/pp/ppval_script.py b/fre/pp/ppval_script.py
index 7481d446d..34750e26f 100644
--- a/fre/pp/ppval_script.py
+++ b/fre/pp/ppval_script.py
@@ -12,6 +12,7 @@
 import netCDF4
 
 from . import nccheck_script as ncc
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -121,7 +122,7 @@ def getenot(date_start: str,
         enot = (diff.days + 1) * 48
 
     else:
-        raise ValueError(f"Unknown chunk_type '{chunk_type}'")
+        log_and_raise(f"Unknown chunk_type '{chunk_type}'")
 
     fre_logger.debug(
         f"date start: {date_start}; date end: {date_end}; "
@@ -184,7 +185,7 @@ def validate(filepath: str):
     try:
         cftime.datetime(1,1,1, calendar = cal)
     except:
-        raise ValueError(f" Calendar name must follow cf convention for validation. {cal} is not a valid calendar.")
+        log_and_raise(f" Calendar name must follow cf convention for validation. {cal} is not a valid calendar.")
 
     # date_{end,start} will have a total of date_end.lastindex groups,
     # that are the year (date_end[1]), the month (date_end[2]), the
@@ -233,7 +234,7 @@ def validate(filepath: str):
 
         # If none of the expected frequencies are found in filepath, raise ValueError
         if all(freq not in path_elements for freq in expected_frequencies):
-            raise ValueError(
+            log_and_raise(
                 f" Cannot determine frequency from {filepath}. Sub-daily"
                 " files must at minimum be placed in a directory"
                 " corresponding to data frequency: '6hr, 'PT6H', '3hr,"
@@ -244,11 +245,11 @@ def validate(filepath: str):
         enot = getenot(date_start, date_end, '30minute', cal)
 
     else:
-        raise ValueError(f"Cannot determine frequency for date '{date_start}'")
+        log_and_raise(f"Cannot determine frequency for date '{date_start}'")
 
     try:
         ncc.check(filepath, enot)
     except:
-        raise ValueError(f"Timesteps found in {filepath} differ from expectation")
+        log_and_raise(f"Timesteps found in {filepath} differ from expectation")
 
     return 0
diff --git a/fre/pp/rename_split_script.py b/fre/pp/rename_split_script.py
index d78a09525..cc92bf78b 100644
--- a/fre/pp/rename_split_script.py
+++ b/fre/pp/rename_split_script.py
@@ -9,6 +9,8 @@
 import yaml
 from metomi.isodatetime.parsers import DurationParser, TimePointParser
 
+from fre import log_and_raise
+
 fre_logger = logging.getLogger(__name__)
 duration_parser = DurationParser()
 time_parser = TimePointParser(assumed_time_zone=(0, 0))
@@ -51,7 +53,7 @@ def get_freq_and_format_from_two_dates(date1: cftime.datetime, date2: cftime.dat
         iso_freq = f"PT{int(minutes)}M"
         format_ = '%Y%m%d%H%M'
     else:
-        raise ValueError(f"Cannot determine frequency and format from '{date1}' and '{date2}'")
+        log_and_raise(f"Cannot determine frequency and format from '{date1}' and '{date2}'")
 
     fre_logger.debug(f"Comparing '{date1}' and '{date2}': returning frequency '{iso_freq}' and format '{format_}'")
     return iso_freq, format_
@@ -82,7 +84,7 @@ def get_duration_from_two_dates(date1: cftime.datetime, date2: cftime.datetime)
         if years_frac < 0.04:
             duration = f"P{years_round}Y"
         else:
-            raise ValueError(f"Could not determine ISO8601 duration between '{date1}' and '{date2}'")
+            log_and_raise(f"Could not determine ISO8601 duration between '{date1}' and '{date2}'")
 
     fre_logger.debug(f"Comparing '{date1}' and '{date2}': returning duration '{duration}'")
     return duration
@@ -121,7 +123,7 @@ def rename_file(input_file: str, diag_manifest: tuple[str, ...] | str | None = (
         var = parts[2]
         tile = None
     else:
-        raise ValueError(f"File '{input_file}' cannot be parsed")
+        log_and_raise(f"File '{input_file}' cannot be parsed")
 
     # open the nc file
     ds = xr.open_dataset(input_file)
@@ -210,19 +212,19 @@ def rename_file(input_file: str, diag_manifest: tuple[str, ...] | str | None = (
                 for manifest in manifests:
                     manifest_path = Path(manifest)
                     if not manifest_path.exists():
-                        raise FileNotFoundError(f"Diag manifest '{manifest}' does not exist")
+                        log_and_raise(f"Diag manifest '{manifest}' does not exist", FileNotFoundError)
                     fre_logger.info(f"Using diag manifest '{manifest}'")
                     with open(manifest_path, 'r') as f:
                         yaml_data = yaml.safe_load(f)
                     for diag_file in yaml_data.get("diag_files", []):
                         if diag_file.get("file_name") == label:
                             if found_entry is not None:
-                                raise Exception(f"Diag file '{label}' found in multiple manifests ('{found_manifest}' and '{manifest}')")
+                                log_and_raise(f"Diag file '{label}' found in multiple manifests ('{found_manifest}' and '{manifest}')", Exception)
                             found_entry = diag_file
                             found_manifest = manifest
 
                 if found_entry is None:
-                    raise Exception(f"File '{label}' not found in diag manifests")
+                    log_and_raise(f"File '{label}' not found in diag manifests", Exception)
 
                 freq_units = found_entry.get("freq_units")
                 freq_value = found_entry.get("freq")
@@ -237,7 +239,7 @@ def rename_file(input_file: str, diag_manifest: tuple[str, ...] | str | None = (
                         duration = f"P{freq_value}M"
                         format_ = "%Y%m"
                 else:
-                    raise Exception(f"Diag manifest found but frequency units '{freq_units}' are unexpected; expected 'years' or 'months'.")
+                    log_and_raise(f"Diag manifest found but frequency units '{freq_units}' are unexpected; expected 'years' or 'months'.", Exception)
 
                 duration_object = duration_parser.parse(duration)
                 # since only one timestep, frequency equals duration
@@ -261,7 +263,7 @@ def rename_file(input_file: str, diag_manifest: tuple[str, ...] | str | None = (
                 freq_label = duration
                 fre_logger.info(f"'{input_file}' has 1 timesteps without diag manifest (legacy case to be removed); date1='{date1}'; date2='{date2}'; duration='{duration}'")
             else:
-                raise ValueError(f"Diag manifest required to process input file '{input_file}' with one timestep and no time bounds")
+                log_and_raise(f"Diag manifest required to process input file '{input_file}' with one timestep and no time bounds")
 
     date1_str = date1.strftime(format_)
     date2_str = date2.strftime(format_)
@@ -356,4 +358,4 @@ def rename_split(input_dir: str, output_dir: str, component: str, use_subdirs: b
             link_or_copy(input_file, output_file)
             did_something = True
     if not did_something:
-        raise FileNotFoundError(f"No '{component}' files were found in '{input_dir}'")
+        log_and_raise(f"No '{component}' files were found in '{input_dir}'", FileNotFoundError)
diff --git a/fre/pp/run_script.py b/fre/pp/run_script.py
index e8cc62da3..b45f0a41f 100644
--- a/fre/pp/run_script.py
+++ b/fre/pp/run_script.py
@@ -4,6 +4,7 @@
 import time
 
 from . import make_workflow_name
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -31,7 +32,7 @@ def pp_run_subtool(experiment = None, platform = None, target = None,
     :type no_wait: boolean
     """
     if None in [experiment, platform, target]:
-        raise ValueError( 'experiment, platform, and target must all not be None.'
+        log_and_raise( 'experiment, platform, and target must all not be None.'
                           'currently, their values are...'
                           f'{experiment} / {platform} / {target}')
 
@@ -66,6 +67,6 @@ def pp_run_subtool(experiment = None, platform = None, target = None,
         capture_output = True ).stdout.decode('utf-8')
 
     if not len(result):
-        raise Exception('Cylc scheduler was started without error but is not running after 30 seconds')
+        log_and_raise('Cylc scheduler was started without error but is not running after 30 seconds', Exception)
 
     fre_logger.info(result)
diff --git a/fre/pp/split_netcdf_script.py b/fre/pp/split_netcdf_script.py
index fed7db58e..3606cad05 100644
--- a/fre/pp/split_netcdf_script.py
+++ b/fre/pp/split_netcdf_script.py
@@ -90,12 +90,7 @@ def split_netcdf(inputDir, outputDir, component, history_source, use_subdirs,
         ydict = yaml.safe_load(Path(yamlfile).read_text())
         vardict = get_variables(ydict, component)
         if vardict is None or history_source not in vardict.keys():
-            fre_logger.error(
-                f"error: either component {component} not defined or "
-                f"source {history_source} not defined under component "
-                f"{component} in yamlfile {yamlfile}."
-            )
-            raise ValueError(
+            log_and_raise(
                 f"error: either component {component} not defined or "
                 f"source {history_source} not defined under component "
                 f"{component} in yamlfile {yamlfile}."
@@ -137,12 +132,12 @@ def split_netcdf(inputDir, outputDir, component, history_source, use_subdirs,
                     files_split += 1
         fre_logger.info(f"{files_split} files split")
         if files_split == 0:
-            fre_logger.error(
+            log_and_raise(
                 f"error: no files found in dirs {sd_string} under "
                 f"{workdir} that match pattern {file_regex}; "
-                "no splitting took place"
+                "no splitting took place",
+                OSError
             )
-            raise OSError
     else:
         files_split = 0
         files=[os.path.join(workdir, el) for el in os.listdir(workdir) if re.match(file_regex, el) is not None]
@@ -151,11 +146,11 @@ def split_netcdf(inputDir, outputDir, component, history_source, use_subdirs,
             split_file_xarray(infile, os.path.abspath(outputDir), varlist)
             files_split += 1
         if len(files) == 0:
-            fre_logger.error(
+            log_and_raise(
                 f"error: no files found in {workdir} that match pattern "
-                f"{file_regex}; no splitting took place"
+                f"{file_regex}; no splitting took place",
+                OSError
             )
-            raise OSError
 
     fre_logger.info(f"split-netcdf-wrapper call complete, having split {files_split} files")
     sys.exit(0) #check this
diff --git a/fre/pp/status_script.py b/fre/pp/status_script.py
index 963fecd4a..35c17054c 100644
--- a/fre/pp/status_script.py
+++ b/fre/pp/status_script.py
@@ -3,6 +3,7 @@
 import subprocess
 import logging
 from . import make_workflow_name
+from fre import log_and_raise
 fre_logger = logging.getLogger(__name__)
 TIMEOUT_SECS=120#30
 
@@ -21,7 +22,7 @@ def status_subtool(experiment = None, platform = None, target = None):
     """
 
     if None in [experiment, platform, target]:
-        raise ValueError( 'experiment, platform, and target must all not be None.'
+        log_and_raise( 'experiment, platform, and target must all not be None.'
                           'currently, their values are...'
                           f'{experiment} / {platform} / {target}')
 
@@ -33,4 +34,4 @@ def status_subtool(experiment = None, platform = None, target = None):
     try:
         subprocess.run(cmd, shell=True, check=True, timeout=TIMEOUT_SECS)
     except:
-        raise Exception('FAILED: subprocess call to- cylc workflow-state {name}')
+        log_and_raise('FAILED: subprocess call to- cylc workflow-state {name}', Exception)
diff --git a/fre/pp/trigger_script.py b/fre/pp/trigger_script.py
index c4e95f0bc..67fa3b762 100644
--- a/fre/pp/trigger_script.py
+++ b/fre/pp/trigger_script.py
@@ -4,6 +4,7 @@
 import subprocess
 
 from . import make_workflow_name
+from fre import log_and_raise
 
 
 fre_logger = logging.getLogger(__name__)
@@ -31,7 +32,7 @@ def trigger(experiment = None, platform = None, target = None, time = None):
         the first chunk of a filename (19790101.atmos_tracer.tile6.nc).
     """
     if None in [experiment, platform, target, time]:
-        raise ValueError( 'experiment, platform, target and time must all not be None.'
+        log_and_raise( 'experiment, platform, target and time must all not be None.'
                           'currently, their values are...'
                           f'{experiment} / {platform} / {target} / {time}')
 
diff --git a/fre/pp/validate_script.py b/fre/pp/validate_script.py
index 7839f72d8..37f525497 100644
--- a/fre/pp/validate_script.py
+++ b/fre/pp/validate_script.py
@@ -3,6 +3,7 @@
 import os
 import subprocess
 from . import make_workflow_name
+from fre import log_and_raise
 
 def validate_subtool(experiment = None, platform = None, target = None):
     """
@@ -10,7 +11,7 @@ def validate_subtool(experiment = None, platform = None, target = None):
     ~/cylc-src/<experiment>__<platform>__<target>
     """
     if None in [experiment, platform, target]:
-        raise ValueError( 'experiment, platform, and target must all not be None.'
+        log_and_raise( 'experiment, platform, and target must all not be None.'
                           'currently, their values are...'
                           f'{experiment} / {platform} / {target}')
 
@@ -26,7 +27,7 @@ def validate_subtool(experiment = None, platform = None, target = None):
         cmd = "rose macro --validate"
         subprocess.run(cmd, shell=True, check=True)
     except:
-        raise Exception('rose macro --validate exited non-zero')
+        log_and_raise('rose macro --validate exited non-zero', Exception)
     finally:
         os.chdir(go_back_here)
 
@@ -38,6 +39,6 @@ def validate_subtool(experiment = None, platform = None, target = None):
         cmd = "cylc validate ."
         subprocess.run(cmd, shell=True, check=True)
     except:
-        raise Exception('cylc validate . exited non-zero')
+        log_and_raise('cylc validate . exited non-zero', Exception)
     finally:
         os.chdir(go_back_here)
diff --git a/fre/run/frerun.py b/fre/run/frerun.py
index 81533bd9d..507cd8e92 100644
--- a/fre/run/frerun.py
+++ b/fre/run/frerun.py
@@ -4,6 +4,7 @@
 
 import click
 from .frerunexample import run_test_function
+from fre import log_and_raise
 
 @click.group(help=click.style(" - run subcommands !!!NotImplemented!!!", fg=(164,29,132)))
 def run_cli():
@@ -14,4 +15,4 @@ def run_cli():
 def function(uppercase):
     """ - Execute fre run test """
     run_test_function(uppercase)
-    raise NotImplementedError('fre run has not been implemented yet!')
+    log_and_raise('fre run has not been implemented yet!', NotImplementedError)

From 74a960304d6b1c6a424f0866d2c5e51c4db56dea Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Apr 2026 05:51:34 +0000
Subject: [PATCH 04/10] Add explicit ValueError to log_and_raise calls

Make exception type explicit in all log_and_raise calls where ValueError
was being raised (matching the original raise ValueError statements).
Also fix a code structure issue in combine.py where the if/elif frequency
blocks were incorrectly nested.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/app/generate_time_averages/combine.py     |  6 +++--
 fre/app/helpers.py                            |  2 +-
 .../remap_pp_components.py                    | 24 ++++++++++---------
 fre/make/create_checkout_script.py            |  4 ++--
 fre/make/create_compile_script.py             |  2 +-
 fre/make/create_docker_script.py              |  2 +-
 fre/make/create_makefile_script.py            |  2 +-
 fre/make/gfdlfremake/platformfre.py           |  6 ++---
 fre/make/gfdlfremake/yamlfre.py               |  2 +-
 fre/make/make_helpers.py                      |  3 ++-
 fre/make/run_fremake_script.py                |  2 +-
 fre/pp/checkout_script.py                     |  4 ++--
 fre/pp/nccheck_script.py                      |  3 ++-
 fre/pp/ppval_script.py                        | 11 +++++----
 fre/pp/rename_split_script.py                 |  8 +++----
 15 files changed, 44 insertions(+), 37 deletions(-)

diff --git a/fre/app/generate_time_averages/combine.py b/fre/app/generate_time_averages/combine.py
index c96c34812..57dfb2ad9 100644
--- a/fre/app/generate_time_averages/combine.py
+++ b/fre/app/generate_time_averages/combine.py
@@ -36,7 +36,7 @@ def form_bronx_directory_name(frequency: str,
     elif frequency == "yr":
         frequency_label = "annual"
     else:
-        log_and_raise(f"Frequency '{frequency}' not recognized or supported")
+        log_and_raise(f"Frequency '{frequency}' not recognized or supported", ValueError)
     return frequency_label + '_' + str(interval_object.years) + 'yr'
 
 
@@ -93,7 +93,9 @@ def combine( root_in_dir: str,
     :rtype: None
     """
     if frequency not in ["yr", "mon"]:
-        log_and_raise(f"Frequency '{frequency}' not recognized or supported")
+        log_and_raise(f"Frequency '{frequency}' not recognized or supported", ValueError)
+
+    if frequency == "yr":
         frequency_iso = "P1Y"
     elif frequency == "mon":
         frequency_iso = "P1M"
diff --git a/fre/app/helpers.py b/fre/app/helpers.py
index 5f878d685..240118299 100644
--- a/fre/app/helpers.py
+++ b/fre/app/helpers.py
@@ -63,7 +63,7 @@ def get_variables(yml: dict, pp_comp: str) -> dict:
     # If the dictionary is empty (no overlap of pp components and components
     # in pp yaml) --> error
     if not src_vars:
-        log_and_raise(f"PP component, {pp_comp}, not found in pp yaml configuration!")
+        log_and_raise(f"PP component, {pp_comp}, not found in pp yaml configuration!", ValueError)
 
     return src_vars
 
diff --git a/fre/app/remap_pp_components/remap_pp_components.py b/fre/app/remap_pp_components/remap_pp_components.py
index 2a74fc93d..44bc91b74 100755
--- a/fre/app/remap_pp_components/remap_pp_components.py
+++ b/fre/app/remap_pp_components/remap_pp_components.py
@@ -33,13 +33,13 @@ def verify_dirs(in_dir: str, out_dir: str):
     if Path(in_dir).is_dir():
         fre_logger.info("Input directory is a valid directory")
     else:
-        log_and_raise(f"Error: Input directory {in_dir} does not exist or is not a valid directory")
+        log_and_raise(f"Error: Input directory {in_dir} does not exist or is not a valid directory", ValueError)
 
     # Verify output directory exists and is a directory
     if Path(out_dir).is_dir():
         fre_logger.info("Output directory is a valid directory")
     else:
-        log_and_raise(f"Error: Output directory {out_dir} does not exist or is not a valid directory")
+        log_and_raise(f"Error: Output directory {out_dir} does not exist or is not a valid directory", ValueError)
 
 def create_dir(out_dir: str, comp: str, freq: str, chunk:str, ens:str, dir_ts: bool) -> str:
     """
@@ -116,7 +116,7 @@ def freq_to_legacy(iso_dura: str) -> str:
     elif iso_dura in ['PT30M', 'PT0.5H']:
         freq_legacy = '30min'
     else:
-        log_and_raise(f"Could not convert ISO duration '{iso_dura}'")
+        log_and_raise(f"Could not convert ISO duration '{iso_dura}'", ValueError)
 
     return freq_legacy
 
@@ -162,7 +162,7 @@ def freq_to_date_format(iso_freq: str) -> str:
     elif (iso_freq[:2]=='PT') and (iso_freq[-1:]=='H'):
         return 'CCYYMMDDThh'
     else:
-        log_and_raise(f'ERROR: Unknown Frequency {iso_freq}')
+        log_and_raise(f'ERROR: Unknown Frequency {iso_freq}', ValueError)
 
 def truncate_date(date: str, freq: str) -> str:
     """
@@ -232,7 +232,7 @@ def search_files(product: str, var: list, source: str, freq: str,
                 fre_logger.info("var: %s", v)
                 f = glob.glob(f"{source}.{v}*.nc")
                 if not f: #if glob returns empty list
-                    log_and_raise("Variable {v} could not be found or does not exist.")
+                    log_and_raise("Variable {v} could not be found or does not exist.", ValueError)
                 files.extend(f)
     else:
         if product == "ts":
@@ -241,7 +241,7 @@ def search_files(product: str, var: list, source: str, freq: str,
         elif product == "av":
             date = truncate_date(begin, "P1Y")
         else:
-            log_and_raise("Product not set to ts or av.")
+            log_and_raise("Product not set to ts or av.", ValueError)
 
         if var == "all":
             f = glob.glob(f"{source}.{date}-*.*.nc")
@@ -251,7 +251,7 @@ def search_files(product: str, var: list, source: str, freq: str,
                 fre_logger.info("var: %s", v)
                 f = glob.glob(f"{source}.{date}-*.{v}*.nc")
                 if not f: #if glob returns empty list
-                    log_and_raise("Variable {v} could not be found or does not exist.")
+                    log_and_raise("Variable {v} could not be found or does not exist.", ValueError)
                 files.extend(f)
         if product == "av" and current_chunk == "P1Y":
             f = glob.glob(f"{source}.{date}.*.nc")
@@ -279,7 +279,8 @@ def get_varlist(comp_info: dict, product: str, req_source: str, src_vars: dict)
         if comp_info.get("static") is None:
             log_and_raise(
                 f"Product is set to static but no static sources/variables defined for "
-                f"{comp_info.get('type')}"
+                f"{comp_info.get('type')}",
+                ValueError
             )
 
     ## Dictionary of variables associated with pp component source name
@@ -543,9 +544,9 @@ def remap_pp_components(input_dir: str, output_dir: str, begin_date: str, curren
 
                             if not files:
                                 if ens_mem is not None:
-                                    log_and_raise(f"\nError: No input files found in {input_dir}/{g}/{ens_mem}/{s}/{f}/{c}")
+                                    log_and_raise(f"\nError: No input files found in {input_dir}/{g}/{ens_mem}/{s}/{f}/{c}", ValueError)
                                 else:
-                                    log_and_raise(f"\nError: No input files found in {input_dir}/{g}/{s}/{f}/{c}")
+                                    log_and_raise(f"\nError: No input files found in {input_dir}/{g}/{s}/{f}/{c}", ValueError)
 
                             os.chdir(output_dir)
 
@@ -593,7 +594,8 @@ def remap_pp_components(input_dir: str, output_dir: str, begin_date: str, curren
                                     if not Path(src_file).exists():
                                         log_and_raise("Offline diagnostic file defined but "
                                                          f"{src_file} does not exist or cannot "
-                                                         "be found!")
+                                                         "be found!",
+                                                         ValueError)
 
                                     offline_link = ["ln",
                                                     "-s",
diff --git a/fre/make/create_checkout_script.py b/fre/make/create_checkout_script.py
index 02ccf6126..615e463a1 100644
--- a/fre/make/create_checkout_script.py
+++ b/fre/make/create_checkout_script.py
@@ -116,7 +116,7 @@ def checkout_create(yamlfile: str, platform: tuple, target: tuple,
     jobs_str = str(njobs)
 
     if isinstance(njobs, bool) and execute:
-        log_and_raise('njobs must be defined as a number if --execute flag is True')
+        log_and_raise('njobs must be defined as a number if --execute flag is True', ValueError)
 
     # Determine backgrounding syntax
     # parallel_cmd is the suffix added to shell commands
@@ -152,7 +152,7 @@ def checkout_create(yamlfile: str, platform: tuple, target: tuple,
 
     for platform_name in platform:
         if not model_yaml.platforms.hasPlatform(platform_name):
-            log_and_raise(f"{platform_name} does not exist in platforms.yaml")
+            log_and_raise(f"{platform_name} does not exist in platforms.yaml", ValueError)
 
         platform_info = model_yaml.platforms.getPlatformFromName(platform_name)
 
diff --git a/fre/make/create_compile_script.py b/fre/make/create_compile_script.py
index 4a50964fd..a66a22bd8 100644
--- a/fre/make/create_compile_script.py
+++ b/fre/make/create_compile_script.py
@@ -102,7 +102,7 @@ def compile_create(yamlfile:str, platform:tuple[str], target:tuple[str], makejob
         for target_name in tlist:
             target = targetfre.fretarget(target_name)
             if not model_yaml.platforms.hasPlatform(platform_name):
-                log_and_raise(f"{platform_name} does not exist in platforms.yaml")
+                log_and_raise(f"{platform_name} does not exist in platforms.yaml", ValueError)
 
             platform = model_yaml.platforms.getPlatformFromName(platform_name)
             ## Make the bld_dir based on the modelRoot, the platform, and the target
diff --git a/fre/make/create_docker_script.py b/fre/make/create_docker_script.py
index 70d670ec0..29cd41f74 100644
--- a/fre/make/create_docker_script.py
+++ b/fre/make/create_docker_script.py
@@ -80,7 +80,7 @@ def dockerfile_create(yamlfile: str, platform: tuple[str], target: tuple[str],
         for targetName in tlist:
             targetObject = targetfre.fretarget(targetName)
             if not modelYaml.platforms.hasPlatform(platformName):
-                log_and_raise(f"{platformName} does not exist in platforms.yaml")
+                log_and_raise(f"{platformName} does not exist in platforms.yaml", ValueError)
 
             platform = modelYaml.platforms.getPlatformFromName(platformName)
 
diff --git a/fre/make/create_makefile_script.py b/fre/make/create_makefile_script.py
index 47bc96349..cbaf0ce18 100644
--- a/fre/make/create_makefile_script.py
+++ b/fre/make/create_makefile_script.py
@@ -93,7 +93,7 @@ def makefile_create(yamlfile: str, platform: tuple[str], target: tuple[str]):
             if model_yaml.platforms.hasPlatform(platform_name):
                 pass
             else:
-                log_and_raise(f"{platform_name} does not exist in platforms.yaml")
+                log_and_raise(f"{platform_name} does not exist in platforms.yaml", ValueError)
 
             platform=model_yaml.platforms.getPlatformFromName(platform_name)
             ## Make the bld_dir based on the modelRoot, the platform, and the target
diff --git a/fre/make/gfdlfremake/platformfre.py b/fre/make/gfdlfremake/platformfre.py
index 898404cdc..854121931 100644
--- a/fre/make/gfdlfremake/platformfre.py
+++ b/fre/make/gfdlfremake/platformfre.py
@@ -55,7 +55,7 @@ def __init__(self,platforminfo):
                 except:
                     log_and_raise("Platform "+p["name"]+": You must specify the program used to build the container (containerBuild) on the "+p["name"]+" platform in the file "+fname+"\n", Exception)
                 if p["containerBuild"] != "podman" and p["containerBuild"] != "docker":
-                    log_and_raise("Platform "+p["name"]+": Container builds only supported with docker or podman, but you listed "+p["containerBuild"]+"\n")
+                    log_and_raise("Platform "+p["name"]+": Container builds only supported with docker or podman, but you listed "+p["containerBuild"]+"\n", ValueError)
                 ## Get the name of the base container
                 try:
                     p["containerBase"]
@@ -80,7 +80,7 @@ def __init__(self,platforminfo):
                     except:
                         p["container2base"] = ""
                     else:
-                        log_and_raise("Platform "+p["name"]+": You defined container2base "+p["container2base"]+" but container2step is False\n")
+                        log_and_raise("Platform "+p["name"]+": You defined container2base "+p["container2base"]+" but container2step is False\n", ValueError)
                 ## Get any commands to execute in the dockerfile RUN command
                 try:
                     p["RUNenv"]
@@ -109,7 +109,7 @@ def __init__(self,platforminfo):
                 try:
                     p["mkTemplate"]
                 except:
-                    log_and_raise("The platform "+p["name"]+" must specify a mkTemplate \n")
+                    log_and_raise("The platform "+p["name"]+" must specify a mkTemplate \n", ValueError)
 
     def hasPlatform(self,name):
         """
diff --git a/fre/make/gfdlfremake/yamlfre.py b/fre/make/gfdlfremake/yamlfre.py
index aca681deb..ef72ee40e 100644
--- a/fre/make/gfdlfremake/yamlfre.py
+++ b/fre/make/gfdlfremake/yamlfre.py
@@ -33,7 +33,7 @@ def __init__(self,compileinfo):
         self.yaml = compileinfo
         # Check if self.yaml is None
         if self.yaml is None:
-            log_and_raise("The provided compileinfo is None. It must be a valid dictionary.")
+            log_and_raise("The provided compileinfo is None. It must be a valid dictionary.", ValueError)
         ## Check for required experiment name
         try:
             self.yaml["experiment"]
diff --git a/fre/make/make_helpers.py b/fre/make/make_helpers.py
index c49d3c7ee..0048a312d 100644
--- a/fre/make/make_helpers.py
+++ b/fre/make/make_helpers.py
@@ -42,7 +42,8 @@ def get_mktemplate_path(mk_template: str, container_flag: bool, model_root: str
         # Check in template path exists
         if not Path(template_path).exists():
             log_and_raise("Error w/ mkmf template. Created path from given "
-                             f"filename: {template_path} does not exist.")
+                             f"filename: {template_path} does not exist.",
+                             ValueError)
     else:
         if "/" not in mk_template:
             template_path = model_root+"/mkmf/templates/"+mk_template
diff --git a/fre/make/run_fremake_script.py b/fre/make/run_fremake_script.py
index a11ac852c..6799201d1 100644
--- a/fre/make/run_fremake_script.py
+++ b/fre/make/run_fremake_script.py
@@ -90,7 +90,7 @@ def fremake_run(yamlfile:str, platform:str, target:str,
     container_platforms = ()
     for platform_name in plist:
         if not model_yaml.platforms.hasPlatform(platform_name):
-            log_and_raise(f"{platform_name} does not exist in platforms.yaml")
+            log_and_raise(f"{platform_name} does not exist in platforms.yaml", ValueError)
 
         platform_info = model_yaml.platforms.getPlatformFromName(platform_name)
 
diff --git a/fre/pp/checkout_script.py b/fre/pp/checkout_script.py
index 8262feec0..63049dc7d 100644
--- a/fre/pp/checkout_script.py
+++ b/fre/pp/checkout_script.py
@@ -52,7 +52,7 @@ def checkout_template(experiment = None, platform = None, target = None, branch
     if None in [experiment, platform, target]:
         os.chdir(go_back_here)
         log_and_raise( 'one of these are None: experiment / platform / target = \n'
-                         f'{experiment} / {platform} / {target}' )
+                         f'{experiment} / {platform} / {target}', ValueError)
     #name = f"{experiment}__{platform}__{target}"
     workflow_name = make_workflow_name(experiment, platform, target)
 
@@ -97,7 +97,7 @@ def checkout_template(experiment = None, platform = None, target = None, branch
             fre_logger.info(
                 f"ERROR: current branch is '{current_branch}', current tag-describe is '{current_tag}'")
             os.chdir(go_back_here)
-            log_and_raise('neither tag nor branch matches the git clone branch arg')
+            log_and_raise('neither tag nor branch matches the git clone branch arg', ValueError)
 
     # make sure we are back where we should be
     if os.getcwd() != go_back_here:
diff --git a/fre/pp/nccheck_script.py b/fre/pp/nccheck_script.py
index 985e77754..ec9df1583 100644
--- a/fre/pp/nccheck_script.py
+++ b/fre/pp/nccheck_script.py
@@ -42,5 +42,6 @@ def check(file_path: str, num_steps: int):
         log_and_raise(
             f" Unexpected number of timesteps found in {file_path}. "
             f"Found: {num_actual_steps} timesteps  "
-            f"Expected: {num_steps} timesteps"
+            f"Expected: {num_steps} timesteps",
+            ValueError
         )
diff --git a/fre/pp/ppval_script.py b/fre/pp/ppval_script.py
index 34750e26f..8a542ba19 100644
--- a/fre/pp/ppval_script.py
+++ b/fre/pp/ppval_script.py
@@ -122,7 +122,7 @@ def getenot(date_start: str,
         enot = (diff.days + 1) * 48
 
     else:
-        log_and_raise(f"Unknown chunk_type '{chunk_type}'")
+        log_and_raise(f"Unknown chunk_type '{chunk_type}'", ValueError)
 
     fre_logger.debug(
         f"date start: {date_start}; date end: {date_end}; "
@@ -185,7 +185,7 @@ def validate(filepath: str):
     try:
         cftime.datetime(1,1,1, calendar = cal)
     except:
-        log_and_raise(f" Calendar name must follow cf convention for validation. {cal} is not a valid calendar.")
+        log_and_raise(f" Calendar name must follow cf convention for validation. {cal} is not a valid calendar.", ValueError)
 
     # date_{end,start} will have a total of date_end.lastindex groups,
     # that are the year (date_end[1]), the month (date_end[2]), the
@@ -238,18 +238,19 @@ def validate(filepath: str):
                 f" Cannot determine frequency from {filepath}. Sub-daily"
                 " files must at minimum be placed in a directory"
                 " corresponding to data frequency: '6hr, 'PT6H', '3hr,"
-                " 'PT3H', '1hr, 'PT1H', '30min, 'PT30M, 'PT0.5H'"
+                " 'PT3H', '1hr, 'PT1H', '30min, 'PT30M, 'PT0.5H'",
+                ValueError
             )
 
     elif date_length == 12:
         enot = getenot(date_start, date_end, '30minute', cal)
 
     else:
-        log_and_raise(f"Cannot determine frequency for date '{date_start}'")
+        log_and_raise(f"Cannot determine frequency for date '{date_start}'", ValueError)
 
     try:
         ncc.check(filepath, enot)
     except:
-        log_and_raise(f"Timesteps found in {filepath} differ from expectation")
+        log_and_raise(f"Timesteps found in {filepath} differ from expectation", ValueError)
 
     return 0
diff --git a/fre/pp/rename_split_script.py b/fre/pp/rename_split_script.py
index cc92bf78b..dcd177a13 100644
--- a/fre/pp/rename_split_script.py
+++ b/fre/pp/rename_split_script.py
@@ -53,7 +53,7 @@ def get_freq_and_format_from_two_dates(date1: cftime.datetime, date2: cftime.dat
         iso_freq = f"PT{int(minutes)}M"
         format_ = '%Y%m%d%H%M'
     else:
-        log_and_raise(f"Cannot determine frequency and format from '{date1}' and '{date2}'")
+        log_and_raise(f"Cannot determine frequency and format from '{date1}' and '{date2}'", ValueError)
 
     fre_logger.debug(f"Comparing '{date1}' and '{date2}': returning frequency '{iso_freq}' and format '{format_}'")
     return iso_freq, format_
@@ -84,7 +84,7 @@ def get_duration_from_two_dates(date1: cftime.datetime, date2: cftime.datetime)
         if years_frac < 0.04:
             duration = f"P{years_round}Y"
         else:
-            log_and_raise(f"Could not determine ISO8601 duration between '{date1}' and '{date2}'")
+            log_and_raise(f"Could not determine ISO8601 duration between '{date1}' and '{date2}'", ValueError)
 
     fre_logger.debug(f"Comparing '{date1}' and '{date2}': returning duration '{duration}'")
     return duration
@@ -123,7 +123,7 @@ def rename_file(input_file: str, diag_manifest: tuple[str, ...] | str | None = (
         var = parts[2]
         tile = None
     else:
-        log_and_raise(f"File '{input_file}' cannot be parsed")
+        log_and_raise(f"File '{input_file}' cannot be parsed", ValueError)
 
     # open the nc file
     ds = xr.open_dataset(input_file)
@@ -263,7 +263,7 @@ def rename_file(input_file: str, diag_manifest: tuple[str, ...] | str | None = (
                 freq_label = duration
                 fre_logger.info(f"'{input_file}' has 1 timesteps without diag manifest (legacy case to be removed); date1='{date1}'; date2='{date2}'; duration='{duration}'")
             else:
-                log_and_raise(f"Diag manifest required to process input file '{input_file}' with one timestep and no time bounds")
+                log_and_raise(f"Diag manifest required to process input file '{input_file}' with one timestep and no time bounds", ValueError)
 
     date1_str = date1.strftime(format_)
     date2_str = date2.strftime(format_)

From 72ec23c921b6d9927a87aca87cb3aa1118244dcb Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Apr 2026 05:57:13 +0000
Subject: [PATCH 05/10] Fix code review issues: restore interval_object
 assignment, add explicit ValueError to log_and_raise calls

- Restore accidentally removed interval_object = duration_parser.parse(interval)
  in combine.py form_bronx_directory_name()
- Add explicit ValueError type to all log_and_raise() calls that relied on the
  default parameter: frenctoolsTimeAverager.py, generate_time_averages.py,
  wrapper.py, mask_atmos_plevel.py, platformfre.py, targetfre.py, cmor_yamler.py

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/app/generate_time_averages/combine.py              |  1 +
 .../generate_time_averages/frenctoolsTimeAverager.py   | 10 +++++-----
 .../generate_time_averages/generate_time_averages.py   |  4 ++--
 fre/app/generate_time_averages/wrapper.py              |  2 +-
 fre/app/mask_atmos_plevel/mask_atmos_plevel.py         |  2 +-
 fre/cmor/cmor_yamler.py                                |  6 +++---
 fre/make/gfdlfremake/platformfre.py                    |  2 +-
 fre/make/gfdlfremake/targetfre.py                      |  6 +++---
 8 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/fre/app/generate_time_averages/combine.py b/fre/app/generate_time_averages/combine.py
index 57dfb2ad9..2bbfbfa99 100644
--- a/fre/app/generate_time_averages/combine.py
+++ b/fre/app/generate_time_averages/combine.py
@@ -37,6 +37,7 @@ def form_bronx_directory_name(frequency: str,
         frequency_label = "annual"
     else:
         log_and_raise(f"Frequency '{frequency}' not recognized or supported", ValueError)
+    interval_object = duration_parser.parse(interval)
     return frequency_label + '_' + str(interval_object.years) + 'yr'
 
 
diff --git a/fre/app/generate_time_averages/frenctoolsTimeAverager.py b/fre/app/generate_time_averages/frenctoolsTimeAverager.py
index 00b05cc36..9bbf4e16b 100644
--- a/fre/app/generate_time_averages/frenctoolsTimeAverager.py
+++ b/fre/app/generate_time_averages/frenctoolsTimeAverager.py
@@ -36,7 +36,7 @@ def generate_timavg(self, infile=None, outfile=None):
         """
         exitstatus=1
         if self.avg_type not in ['month','all']:
-            log_and_raise(f'avg_type= {self.avg_type} not supported by this class at this time.')
+            log_and_raise(f'avg_type= {self.avg_type} not supported by this class at this time.', ValueError)
 
         if self.unwgt:
             fre_logger.warning('unwgt=True unsupported by frenctoolsAverager. Ignoring!!!')
@@ -46,7 +46,7 @@ def generate_timavg(self, infile=None, outfile=None):
                    ' not currently supported for frenctols time averaging. ignoring!', self.var)
 
         if infile is None:
-            log_and_raise('Need an input file, specify a value for the infile argument')
+            log_and_raise('Need an input file, specify a value for the infile argument', ValueError)
 
         if outfile is None:
             outfile='frenctoolsTimeAverage_'+infile
@@ -54,7 +54,7 @@ def generate_timavg(self, infile=None, outfile=None):
 
         #check for existence of timavg.csh. If not found, issue might be that user is not in env with frenctools.
         if shutil.which('timavg.csh') is None:
-            log_and_raise('did not find timavg.csh')
+            log_and_raise('did not find timavg.csh', ValueError)
         fre_logger.info('timeaverager using: %s', shutil.which("timavg.csh"))
 
 
@@ -107,7 +107,7 @@ def generate_timavg(self, infile=None, outfile=None):
 
                     if subp.returncode != 0:
                         fre_logger.error('stderror = %s', stderror)
-                        log_and_raise(f'error: timavg.csh had a problem, subp.returncode = {subp.returncode}')
+                        log_and_raise(f'error: timavg.csh had a problem, subp.returncode = {subp.returncode}', ValueError)
 
                     fre_logger.info('%s climatology successfully ran',nc_monthly_file)
                     exitstatus=0
@@ -131,7 +131,7 @@ def generate_timavg(self, infile=None, outfile=None):
 
             if subp.returncode != 0:
                 fre_logger.error('stderror  = %s', stderror)
-                log_and_raise(f'error: timavgcsh command not properly executed, subp.returncode = {subp.returncode}')
+                log_and_raise(f'error: timavgcsh command not properly executed, subp.returncode = {subp.returncode}', ValueError)
 
             fre_logger.info('climatology successfully ran')
             exitstatus = 0
diff --git a/fre/app/generate_time_averages/generate_time_averages.py b/fre/app/generate_time_averages/generate_time_averages.py
index 196fb0a47..bafaf1cf9 100755
--- a/fre/app/generate_time_averages/generate_time_averages.py
+++ b/fre/app/generate_time_averages/generate_time_averages.py
@@ -42,9 +42,9 @@ def generate_time_average(infile: Union[str, List[str]] = None,
     start_time = time.perf_counter()
     fre_logger.debug('called generate_time_average')
     if None in [infile, outfile, pkg]:
-        log_and_raise('infile, outfile, and pkg are required inputs')
+        log_and_raise('infile, outfile, and pkg are required inputs', ValueError)
     if pkg not in ['cdo', 'fre-nctools', 'fre-python-tools']:
-        log_and_raise(f'argument pkg = {pkg} not known, must be one of: cdo, fre-nctools, fre-python-tools')
+        log_and_raise(f'argument pkg = {pkg} not known, must be one of: cdo, fre-nctools, fre-python-tools', ValueError)
     exitstatus = 1
     myavger = None
 
diff --git a/fre/app/generate_time_averages/wrapper.py b/fre/app/generate_time_averages/wrapper.py
index 2609be7e5..13fa3e551 100644
--- a/fre/app/generate_time_averages/wrapper.py
+++ b/fre/app/generate_time_averages/wrapper.py
@@ -78,7 +78,7 @@ def generate_wrapper(cycle_point: str,
     input_interval = DurationParser().parse(input_interval)
 
     if frequency not in ["yr", "mon"]:
-        log_and_raise(f"Frequency '{frequency}' not recognized or supported")
+        log_and_raise(f"Frequency '{frequency}' not recognized or supported", ValueError)
 
     # convert frequency 'yr' or 'mon' to ISO8601
     if frequency == 'mon':
diff --git a/fre/app/mask_atmos_plevel/mask_atmos_plevel.py b/fre/app/mask_atmos_plevel/mask_atmos_plevel.py
index 9f47a0f91..df00d9f92 100755
--- a/fre/app/mask_atmos_plevel/mask_atmos_plevel.py
+++ b/fre/app/mask_atmos_plevel/mask_atmos_plevel.py
@@ -64,7 +64,7 @@ def mask_atmos_plevel_subtool(infile: str = None,
     if "ps" not in list(ds_ps.variables):
         fre_logger.warning('pressure variable ps not found in target pressure file')
         if not warn_no_ps:
-            log_and_raise(f"Surface pressure file {psfile} does not contain surface pressure.")
+            log_and_raise(f"Surface pressure file {psfile} does not contain surface pressure.", ValueError)
         fre_logger.warning('warn_no_ps is True! this means I\'m going to no-op gracefully instead of raising an error')
         return
 
diff --git a/fre/cmor/cmor_yamler.py b/fre/cmor/cmor_yamler.py
index a4549dece..414fb284e 100644
--- a/fre/cmor/cmor_yamler.py
+++ b/fre/cmor/cmor_yamler.py
@@ -183,7 +183,7 @@ def cmor_yaml_subtool( yamlfile: str = None,
                 log_and_raise(
                     f'freq is required for CMIP7 but was not specified for table target {table_name}.\n'
                     f'  CMIP7 MIP tables do not contain frequency metadata.\n'
-                    f'  please set freq explicitly (e.g. "monthly", "daily") in the cmor yaml.')
+                    f'  please set freq explicitly (e.g. "monthly", "daily") in the cmor yaml.', ValueError)
             # CMIP6 tables carry frequency — attempt to derive it
             fre_logger.info('freq not specified in cmor yaml for table %s, '
                             'attempting to derive from CMIP6 MIP table', table_name)
@@ -195,7 +195,7 @@ def cmor_yaml_subtool( yamlfile: str = None,
                 log_and_raise(
                     f'not enough frequency information to process variables for {table_name}.\n'
                     f'  freq was not specified in the cmor yaml, and could not be derived from the MIP table.\n'
-                    f'  please set freq explicitly (e.g. "monthly", "daily") in the cmor yaml.')
+                    f'  please set freq explicitly (e.g. "monthly", "daily") in the cmor yaml.', ValueError)
             fre_logger.info('derived freq = %s from MIP table %s', freq, json_mip_table_config)
 
         # update the table target dict so downstream code sees the resolved freq
@@ -211,7 +211,7 @@ def cmor_yaml_subtool( yamlfile: str = None,
             grid_desc = gridding_dict['grid_desc']
             nom_res = gridding_dict['nom_res']
             if None in [grid_label, grid_desc, nom_res]:
-                log_and_raise('gridding dictionary, if present, must have all three fields be non-empty.')
+                log_and_raise('gridding dictionary, if present, must have all three fields be non-empty.', ValueError)
         # gridding info of data ---- revisit
 
         table_components_list = cmor_yaml_table_target['target_components']
diff --git a/fre/make/gfdlfremake/platformfre.py b/fre/make/gfdlfremake/platformfre.py
index 854121931..29bc2a966 100644
--- a/fre/make/gfdlfremake/platformfre.py
+++ b/fre/make/gfdlfremake/platformfre.py
@@ -97,7 +97,7 @@ def __init__(self,platforminfo):
                 except:
                     log_and_raise("You must specify the program used to run the container (containerRun) on the "+p["name"]+" platform in the file "+fname+"\n", Exception)
                 if p["containerRun"] != "apptainer" and p["containerRun"] != "singularity":
-                    log_and_raise("Container builds only supported with apptainer, but you listed "+p["containerRun"]+"\n")
+                    log_and_raise("Container builds only supported with apptainer, but you listed "+p["containerRun"]+"\n", ValueError)
 
                 ## Get the path to where the output model container will be located
                 try:
diff --git a/fre/make/gfdlfremake/targetfre.py b/fre/make/gfdlfremake/targetfre.py
index 4f5363228..37519e9ec 100644
--- a/fre/make/gfdlfremake/targetfre.py
+++ b/fre/make/gfdlfremake/targetfre.py
@@ -54,19 +54,19 @@ def __init__(self,t):
         if self.debug:
             try:
                 if self.repro or self.prod == True:
-                    log_and_raise(errormsg)
+                    log_and_raise(errormsg, ValueError)
             except ValueError:
                 raise
         elif self.repro:
             try:
                 if self.prod == True:
-                    log_and_raise(errormsg)
+                    log_and_raise(errormsg, ValueError)
             except ValueError:
                 raise
         else:
             try:
                 if self.prod == False:
-                    log_and_raise("Your target '"+self.target+"' needs to include one of the following: prod, repro, debug")
+                    log_and_raise("Your target '"+self.target+"' needs to include one of the following: prod, repro, debug", ValueError)
             except ValueError:
                 raise
 

From e184940bcaa4c12f1c034b2eef7701f99df5ab7f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Apr 2026 06:11:17 +0000
Subject: [PATCH 06/10] Convert raise statements to log_and_raise across 11
 files

Replace all raise ExcType(msg) and raise ExcType(msg) from exc patterns
with log_and_raise(msg, ExcType) and log_and_raise(msg, ExcType, exc=exc)
respectively, across:

- fre/pp/configure_script_yaml.py (already had import)
- fre/cmor/cmor_helpers.py (already had import)
- fre/cmor/cmor_mixer.py (already had import)
- fre/cmor/cmor_finder.py (added import)
- fre/cmor/cmor_config.py (added import)
- fre/yamltools/helpers.py (added import)
- fre/yamltools/info_parsers/cmor_info_parser.py (added import)
- fre/yamltools/info_parsers/compile_info_parser.py (added import)
- fre/yamltools/info_parsers/analysis_info_parser.py (added import)
- fre/yamltools/info_parsers/pp_info_parser.py (added import)
- fre/yamltools/combine_yamls_script.py (added import)

Also converts printf-style multi-arg ValueError/FileNotFoundError calls
to f-string log_and_raise equivalents.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/cmor/cmor_config.py                       | 11 ++--
 fre/cmor/cmor_finder.py                       | 13 ++--
 fre/cmor/cmor_helpers.py                      | 23 ++++---
 fre/cmor/cmor_mixer.py                        | 61 ++++++++++---------
 fre/pp/configure_script_yaml.py               | 12 ++--
 fre/yamltools/combine_yamls_script.py         | 11 ++--
 fre/yamltools/helpers.py                      | 11 ++--
 .../info_parsers/analysis_info_parser.py      | 11 ++--
 .../info_parsers/cmor_info_parser.py          | 17 +++---
 .../info_parsers/compile_info_parser.py       | 11 ++--
 fre/yamltools/info_parsers/pp_info_parser.py  | 13 ++--
 11 files changed, 103 insertions(+), 91 deletions(-)

diff --git a/fre/cmor/cmor_config.py b/fre/cmor/cmor_config.py
index e49fb0bdd..a2f638897 100644
--- a/fre/cmor/cmor_config.py
+++ b/fre/cmor/cmor_config.py
@@ -18,6 +18,7 @@
 import logging
 from pathlib import Path
 
+from fre import log_and_raise
 from .cmor_finder import make_simple_varlist
 from .cmor_constants import EXCLUDED_TABLE_SUFFIXES
 
@@ -103,11 +104,11 @@ def cmor_config_subtool(
     """
     # ---- validate inputs ----
     if not Path(pp_dir).is_dir():
-        raise FileNotFoundError(f'pp_dir does not exist: {pp_dir}')
+        log_and_raise(f'pp_dir does not exist: {pp_dir}', FileNotFoundError)
     if not Path(mip_tables_dir).is_dir():
-        raise FileNotFoundError(f'mip_tables_dir does not exist: {mip_tables_dir}')
+        log_and_raise(f'mip_tables_dir does not exist: {mip_tables_dir}', FileNotFoundError)
     if not Path(exp_config).is_file():
-        raise FileNotFoundError(f'exp_config does not exist: {exp_config}')
+        log_and_raise(f'exp_config does not exist: {exp_config}', FileNotFoundError)
 
     # ensure output directories exist
     Path(varlist_dir).mkdir(parents=True, exist_ok=True)
@@ -116,8 +117,8 @@ def cmor_config_subtool(
     # ---- gather MIP tables ----
     mip_tables = _filter_mip_tables(mip_tables_dir, mip_era)
     if not mip_tables:
-        raise ValueError(
-            f'no MIP tables found in {mip_tables_dir} for era {mip_era} after filtering')
+        log_and_raise(
+            f'no MIP tables found in {mip_tables_dir} for era {mip_era} after filtering', ValueError)
 
     # ---- discover pp components ----
     ppcompdirs = sorted(glob.glob(f'{pp_dir}/*'))
diff --git a/fre/cmor/cmor_finder.py b/fre/cmor/cmor_finder.py
index 55e6ee45a..023928c2d 100644
--- a/fre/cmor/cmor_finder.py
+++ b/fre/cmor/cmor_finder.py
@@ -26,6 +26,7 @@
 from typing import Optional, Dict, IO
 from .cmor_helpers import get_json_file_data
 
+from fre import log_and_raise
 from .cmor_constants import DO_NOT_PRINT_LIST
 
 fre_logger = logging.getLogger(__name__)
@@ -97,12 +98,12 @@ def cmor_find_subtool( json_var_list: Optional[str] = None,
               CMIP6 tables. Information is printed via the logger.
     """
     if not Path(json_table_config_dir).exists():
-        raise OSError(f'ERROR directory {json_table_config_dir} does not exist! exit.')
+        log_and_raise(f'ERROR directory {json_table_config_dir} does not exist! exit.', OSError)
 
     fre_logger.info('attempting to find and open files in dir: \n %s ', json_table_config_dir)
     json_table_configs = glob.glob(f'{json_table_config_dir}/*.json')
     if not json_table_configs:
-        raise OSError(f'ERROR directory {json_table_config_dir} contains no JSON files, exit.')
+        log_and_raise(f'ERROR directory {json_table_config_dir} contains no JSON files, exit.', OSError)
     fre_logger.info('found content in json_table_config_dir')
 
     var_list = None
@@ -111,7 +112,7 @@ def cmor_find_subtool( json_var_list: Optional[str] = None,
             var_list = json.load(var_list_file)
 
     if opt_var_name is None and var_list is None:
-        raise ValueError('ERROR: no opt_var_name given but also no content in variable list!!! exit!')
+        log_and_raise('ERROR: no opt_var_name given but also no content in variable list!!! exit!', ValueError)
 
     if opt_var_name is not None:
         fre_logger.info('opt_var_name is not None: looking for only ONE variables worth of info!')
@@ -172,8 +173,8 @@ def make_simple_varlist( dir_targ: str,
             full_mip_vars_list=get_json_file_data(json_mip_table)["variable_entry"].keys()
 
         except Exception as exc:
-            raise Exception( 'problem opening mip table and getting variable entry data.'
-                            f'exc = {exc}') from exc
+            log_and_raise('problem opening mip table and getting variable entry data.'
+                          f'exc = {exc}', Exception, exc=exc)
 
         fre_logger.debug('attempting to make mip variable list')
         mip_vars=[ key.split('_')[0] for key in full_mip_vars_list ]
@@ -201,5 +202,5 @@ def make_simple_varlist( dir_targ: str,
             with open(output_variable_list, 'w', encoding='utf-8') as f:
                 json.dump(var_list, f, indent=4)
         except Exception as exc:
-            raise OSError('output variable list created but cannot be written') from exc
+            log_and_raise('output variable list created but cannot be written', OSError, exc=exc)
     return var_list
diff --git a/fre/cmor/cmor_helpers.py b/fre/cmor/cmor_helpers.py
index f60425eb3..3276562af 100644
--- a/fre/cmor/cmor_helpers.py
+++ b/fre/cmor/cmor_helpers.py
@@ -247,7 +247,7 @@ def create_lev_bnds( bound_these: Variable = None,
     .. note:: Logs debug information about the input and output arrays.
     """
     if len(with_these) != (len(bound_these) + 1):
-        raise ValueError('failed creating bnds on-the-fly :-(')
+        log_and_raise('failed creating bnds on-the-fly :-(', ValueError)
     fre_logger.debug('bound_these = \n%s', bound_these)
     fre_logger.debug('with_these = \n%s', with_these)
 
@@ -294,8 +294,7 @@ def get_iso_datetime_ranges( var_filenames: List[str],
     fre_logger.debug(' stop_yr_int = %s', stop_yr_int)
 
     if iso_daterange_arr is None:
-        raise ValueError(
-            'this function requires the list one desires to fill with datetime ranges from filenames')
+        log_and_raise('this function requires the list one desires to fill with datetime ranges from filenames', ValueError)
 
     for filename in var_filenames:
         fre_logger.debug('filename = %s', filename)
@@ -316,7 +315,7 @@ def get_iso_datetime_ranges( var_filenames: List[str],
     iso_daterange_arr.sort()
 
     if len(iso_daterange_arr) < 1:
-        raise ValueError('iso_daterange_arr has length 0! i need to find at least one datetime range!')
+        log_and_raise('iso_daterange_arr has length 0! i need to find at least one datetime range!', ValueError)
 
 
 def check_dataset_for_ocean_grid( ds: Dataset) -> bool:
@@ -406,7 +405,7 @@ def create_tmp_dir( outdir: str,
                 fre_logger.info('attempting to create %s dir in tmp_dir targ did not work', outdir_from_exp_config)
                 fre_logger.info('... attempt to avoid a toothless cmor warning failed... moving on')
     except Exception as exc:
-        raise OSError('problem creating tmp output directory {}. stop.'.format(tmp_dir)) from exc
+        log_and_raise('problem creating tmp output directory {}. stop.'.format(tmp_dir), OSError, exc=exc)
 
     return tmp_dir
 
@@ -425,10 +424,10 @@ def get_json_file_data( json_file_path: Optional[str] = None) -> dict:
         with open(json_file_path, "r", encoding="utf-8") as json_config_file:
             return json.load(json_config_file)
     except Exception as exc:
-        raise FileNotFoundError(
+        log_and_raise(
             'ERROR: json_file_path file cannot be opened.\n'
-            '       json_file_path = {}'.format(json_file_path)
-        ) from exc
+            '       json_file_path = {}'.format(json_file_path),
+            FileNotFoundError, exc=exc)
 
 
 def update_grid_and_label( json_file_path: str,
@@ -573,7 +572,7 @@ def check_path_existence(some_path: str):
     :raises FileNotFoundError: If the path does not exist.
     """
     if not Path(some_path).exists():
-        raise FileNotFoundError(f'does not exist:  {some_path}')
+        log_and_raise(f'does not exist:  {some_path}', FileNotFoundError)
 
 def iso_to_bronx_chunk(cmor_chunk_in: str) -> str:
     """
@@ -589,7 +588,7 @@ def iso_to_bronx_chunk(cmor_chunk_in: str) -> str:
     if cmor_chunk_in[0] == 'P' and cmor_chunk_in[-1] == 'Y':
         bronx_chunk = f'{cmor_chunk_in[1:-1]}yr'
     else:
-        raise ValueError('problem with converting to bronx chunk from the cmor chunk. check cmor_yamler.py')
+        log_and_raise('problem with converting to bronx chunk from the cmor chunk. check cmor_yamler.py', ValueError)
     fre_logger.debug('bronx_chunk = %s', bronx_chunk)
     return bronx_chunk
 
@@ -625,7 +624,7 @@ def conv_mip_to_bronx_freq(cmor_table_freq: str) -> Optional[str]:
     if bronx_freq is None:
         fre_logger.warning('MIP table frequency = %s does not have a FRE-bronx equivalent', cmor_table_freq)
     if cmor_table_freq not in cmor_to_bronx_dict.keys():
-        raise KeyError(f'MIP table frequency = "{cmor_table_freq}" is not a valid MIP frequency')
+        log_and_raise(f'MIP table frequency = "{cmor_table_freq}" is not a valid MIP frequency', KeyError)
     return bronx_freq
 
 def get_bronx_freq_from_mip_table(json_table_config: str) -> str:
@@ -646,7 +645,7 @@ def get_bronx_freq_from_mip_table(json_table_config: str) -> str:
                 table_freq = table_config_data['variable_entry'][var_entry]['frequency']
                 break
             except Exception as exc:
-                raise KeyError('no frequency in table under variable_entry. this may be a CMIP7 table.') from exc
+                log_and_raise('no frequency in table under variable_entry. this may be a CMIP7 table.', KeyError, exc=exc)
 
     bronx_freq = conv_mip_to_bronx_freq(table_freq)
     return bronx_freq
diff --git a/fre/cmor/cmor_mixer.py b/fre/cmor/cmor_mixer.py
index ae5d0611f..7dbf78adb 100755
--- a/fre/cmor/cmor_mixer.py
+++ b/fre/cmor/cmor_mixer.py
@@ -208,8 +208,8 @@ def rewrite_netcdf_file_var( mip_var_cfgs: dict = None,
         with open(json_exp_config, "r", encoding="utf-8") as file:
             exp_cfg_calendar = json.load(file)['calendar']
             if exp_cfg_calendar != time_coords_calendar:
-                raise ValueError(f"data calendar type {time_coords_calendar} "
-                                 f"does not match input config calendar type: {exp_cfg_calendar}")
+                log_and_raise(f"data calendar type {time_coords_calendar} "
+                              f"does not match input config calendar type: {exp_cfg_calendar}", ValueError)
 
     # read in time_bnds, if present
     fre_logger.info('attempting to read coordinate BNDS, time_bnds')
@@ -224,7 +224,7 @@ def rewrite_netcdf_file_var( mip_var_cfgs: dict = None,
     lev_bnds = None
     if vert_dim != 0:
         if vert_dim.lower() not in ACCEPTED_VERT_DIMS:
-            raise ValueError(f'var_dim={var_dim}, vert_dim = {vert_dim} is not supported') #uncovered
+            log_and_raise(f'var_dim={var_dim}, vert_dim = {vert_dim} is not supported', ValueError) #uncovered
         lev = ds[vert_dim]
         if vert_dim.lower() != "landuse":
             lev_units = ds[vert_dim].units
@@ -255,7 +255,7 @@ def rewrite_netcdf_file_var( mip_var_cfgs: dict = None,
                 'an ocean statics file is needed, but it could not be found.\n'
                 '   moving on and doing my best, but I am probably going to break'
             )
-            raise FileNotFoundError('statics file not found.') from exc
+            log_and_raise('statics file not found.', FileNotFoundError, exc=exc)
 
 
         fre_logger.info("statics file found.")
@@ -355,14 +355,14 @@ def rewrite_netcdf_file_var( mip_var_cfgs: dict = None,
 
         if any( [yh_dim != (yq_dim - 1),
                  xh_dim != (xq_dim - 1)]):
-            raise ValueError( #uncovered
+            log_and_raise( #uncovered
                 'the number of h-point lat/lon coordinates is inconsistent with the number of\n'
                 'q-point lat/lon coordinates! i.e. ( hpoint_dim != qpoint_dim-1 )\n'
                 f'yh_dim = {yh_dim}\n'
                 f'xh_dim = {xh_dim}\n'
                 f'yq_dim = {yq_dim}\n'
-                f'xq_dim = {xq_dim}'
-            )
+                f'xq_dim = {xq_dim}',
+                ValueError)
 
         # create h-point bounds from the q-point lat lons
         fre_logger.info('creating yh_bnds, xh_bnds from yq, xq')
@@ -763,14 +763,14 @@ def cmorize_target_var_files(indir: str = None,
         make_cmor_write_here = tmp_dir
         # make sure we know where we are writing, or else!
         if not Path(make_cmor_write_here).exists():
-            raise ValueError(f'\ntmp_dir = \n{tmp_dir}\ncannot be found/created/resolved!') #uncovered
+            log_and_raise(f'\ntmp_dir = \n{tmp_dir}\ncannot be found/created/resolved!', ValueError) #uncovered
 
         gotta_go_back_here = os.getcwd()
         try:
             fre_logger.warning("changing directory to: \n%s", make_cmor_write_here)
             os.chdir(make_cmor_write_here)
         except Exception as exc: #uncovered
-            raise OSError(f'(cmorize_target_var_files) could not chdir to {make_cmor_write_here}') from exc
+            log_and_raise(f'(cmorize_target_var_files) could not chdir to {make_cmor_write_here}', OSError, exc=exc)
 
         fre_logger.info("calling rewrite_netcdf_file_var")
         try:
@@ -782,10 +782,11 @@ def cmorize_target_var_files(indir: str = None,
                                                       json_table_config,
                                                       prev_path=nc_fls[i] )
         except Exception as exc: #uncovered
-            raise Exception(
+            log_and_raise(
                 'problem with rewrite_netcdf_file_var. '
                 f'exc={exc}\n'
-                'exiting and executing finally block.') from exc
+                'exiting and executing finally block.',
+                Exception, exc=exc)
         finally:  # should always execute, errors or not!
             fre_logger.warning('finally, changing directory to: \n%s', gotta_go_back_here)
             os.chdir(gotta_go_back_here)
@@ -795,8 +796,8 @@ def cmorize_target_var_files(indir: str = None,
         # now that CMOR has rewritten things... we can take our post-rewriting actions
         # first, remove /CMOR_tmp/ from the output path.
         if not Path(local_file_name).is_absolute():
-            raise ValueError(f'local_file_name should be an absolute path, not a relative one. \n '
-                             f'local_file_name = {local_file_name}')
+            log_and_raise(f'local_file_name should be an absolute path, not a relative one. \n '
+                          f'local_file_name = {local_file_name}', ValueError)
 
         fre_logger.info('local_file_name = %s', local_file_name)
         filename = local_file_name.replace('/CMOR_tmp/','/')
@@ -958,26 +959,28 @@ def cmor_run_subtool(indir: str = None,
     """
     # CHECK req'd inputs
     if None in [indir, json_var_list, json_table_config, json_exp_config, outdir]:
-        raise ValueError('the following input arguments are required:\n'
-                         '[indir, json_var_list, json_table_config, json_exp_config, outdir] = \n'
-                         '[%s, %s, %s, %s, %s]', indir, json_var_list, json_table_config, json_exp_config, outdir)
+        log_and_raise(f'the following input arguments are required:\n'
+                      f'[indir, json_var_list, json_table_config, json_exp_config, outdir] = \n'
+                      f'[{indir}, {json_var_list}, {json_table_config}, {json_exp_config}, {outdir}]',
+                      ValueError)
 
     # CHECK existence of the exp-specific metadata file
     if Path(json_exp_config).exists():
         json_exp_config = str(Path(json_exp_config).resolve())
     else:
-        raise FileNotFoundError('ERROR: json_exp_config file cannot be opened.\n'
-                                'json_exp_config = %s', json_exp_config)
+        log_and_raise(f'ERROR: json_exp_config file cannot be opened.\n'
+                      f'json_exp_config = {json_exp_config}',
+                      FileNotFoundError)
 
     # CHECK mip_era entry of exp config exists, needed ?
     try:
         exp_cfg_mip_era = get_json_file_data(json_exp_config)['mip_era'].upper()
     except KeyError as exc:
-        raise KeyError('no mip_era entry in experimental metadata configuration, the file is noncompliant!') from exc
+        log_and_raise('no mip_era entry in experimental metadata configuration, the file is noncompliant!', KeyError, exc=exc)
 
     fre_logger.debug('exp_cfg_mip_era = %s', exp_cfg_mip_era)
     if exp_cfg_mip_era not in ['CMIP6', 'CMIP7']:
-        raise ValueError('cmor_mixer only supports CMIP6 and CMIP7 cases')
+        log_and_raise('cmor_mixer only supports CMIP6 and CMIP7 cases', ValueError)
 
     if exp_cfg_mip_era == 'CMIP7':
         fre_logger.warning('CMIP7 configuration detected, will be expecting and enforcing variable brands.')
@@ -1013,7 +1016,7 @@ def cmor_run_subtool(indir: str = None,
         mip_var_list = [ var.split('_')[0] for var in mip_fullvar_list ]
         mip_var_brand_list = [ var.split('_')[1] for var in mip_fullvar_list ]
         if len(mip_var_list) != len(mip_var_brand_list):
-            raise ValueError('the number of brands is not one-to-one with the number of variables. check config.')
+            log_and_raise('the number of brands is not one-to-one with the number of variables. check config.', ValueError)
     elif exp_cfg_mip_era == "CMIP6":
         mip_var_list = mip_fullvar_list
 
@@ -1049,13 +1052,15 @@ def cmor_run_subtool(indir: str = None,
 
     # CHECK that there's at least one variable to run after comparing use inputs vars to MIP config input vars
     if len(vars_to_run) < 1:
-        raise ValueError('runnable variable list is of length 0 '
-                         'this means no variables in input variable list are in '
-                         'the mip table configuration, so there\'s nothing to process!')
+        log_and_raise('runnable variable list is of length 0 '
+                      'this means no variables in input variable list are in '
+                      'the mip table configuration, so there\'s nothing to process!',
+                      ValueError)
     if all([opt_var_name is not None, opt_var_name not in list(vars_to_run.keys())]):
-        raise ValueError('opt_var_name is not None! (== %s)'
-                         '... but the variable is not contained in the target mip table'
-                         '... there\'s nothing to process, exit', opt_var_name)
+        log_and_raise(f'opt_var_name is not None! (== {opt_var_name})'
+                      '... but the variable is not contained in the target mip table'
+                      '... there\'s nothing to process, exit',
+                      ValueError)
 
     fre_logger.info('runnable variable list formed, it is vars_to_run=\n%s', vars_to_run)
 
@@ -1065,7 +1070,7 @@ def cmor_run_subtool(indir: str = None,
     indir_filenames = glob.glob(f'{indir}/*.nc')
     indir_filenames.sort()
     if len(indir_filenames) == 0:
-        raise ValueError('no files in input target directory = indir = \n%s', indir)
+        log_and_raise(f'no files in input target directory = indir = \n{indir}', ValueError)
     fre_logger.debug('found %s filenames', len(indir_filenames))
 
     # name_of_set == component label
diff --git a/fre/pp/configure_script_yaml.py b/fre/pp/configure_script_yaml.py
index 86538104d..37d501bcd 100644
--- a/fre/pp/configure_script_yaml.py
+++ b/fre/pp/configure_script_yaml.py
@@ -50,11 +50,11 @@ def validate_yaml(yamlfile: dict) -> None:
         validate(instance = yamlfile,schema=schema)
         fre_logger.info("Combined yaml valid")
     except SchemaError as exc:
-        raise ValueError(f"Schema '{schema_path}' is not valid. Contact the FRE team.") from exc
+        log_and_raise(f"Schema '{schema_path}' is not valid. Contact the FRE team.", ValueError, exc=exc)
     except ValidationError as exc:
-        raise ValueError("Combined yaml is not valid. Please fix the errors and try again.") from exc
+        log_and_raise("Combined yaml is not valid. Please fix the errors and try again.", ValueError, exc=exc)
     except Exception as exc:
-        raise ValueError("Unclear error from validation. Please try to find the error and try again.") from exc
+        log_and_raise("Unclear error from validation. Please try to find the error and try again.", ValueError, exc=exc)
 
 ####################
 def rose_init(experiment: str, platform: str, target: str) -> metomi.rose.config.ConfigNode:
@@ -219,9 +219,9 @@ def yaml_info(yamlfile: str = None, experiment: str = None, platform: str = None
     fre_logger.info('Starting')
 
     if None in [yamlfile, experiment, platform, target]:
-        raise ValueError( 'yamlfile, experiment, platform, and target must all not be None.'
-                          'currently, their values are...'
-                          f'{yamlfile} / {experiment} / {platform} / {target}')
+        log_and_raise('yamlfile, experiment, platform, and target must all not be None.'
+                      'currently, their values are...'
+                      f'{yamlfile} / {experiment} / {platform} / {target}', ValueError)
     e = experiment
     p = platform
     t = target
diff --git a/fre/yamltools/combine_yamls_script.py b/fre/yamltools/combine_yamls_script.py
index 3b4af30a8..cf6d755ac 100755
--- a/fre/yamltools/combine_yamls_script.py
+++ b/fre/yamltools/combine_yamls_script.py
@@ -33,6 +33,7 @@
 #import logging
 #from typing import Optional
 
+from fre import log_and_raise
 from fre.yamltools.info_parsers import cmor_info_parser as cmip
 from fre.yamltools.info_parsers import compile_info_parser as cip
 from fre.yamltools.info_parsers import pp_info_parser as ppip
@@ -85,7 +86,7 @@ def get_combined_cmoryaml( yamlfile: Union[str, Path],
         #fre_logger.debug('...CmorYaml =\n %s...', pformat(CmorYaml))
         #assert False # good.
     except Exception as exc:
-        raise ValueError("CMORYaml.combine_model failed") from exc
+        log_and_raise("CMORYaml.combine_model failed", ValueError, exc=exc)
 
 
     # Merge cmor experiment yamls into combined file, calls experiment_check
@@ -97,7 +98,7 @@ def get_combined_cmoryaml( yamlfile: Union[str, Path],
         #fre_logger.debug('... yaml_content = ...\n %s', pformat(yaml_content))
         #assert False # good.
     except Exception as exc:
-        raise Exception(f"CmorYaml.combine_model failed for some reason.\n exc =\n {exc}") from exc
+        log_and_raise(f"CmorYaml.combine_model failed for some reason.\n exc =\n {exc}", Exception, exc=exc)
 
 
     # settings.yaml is deprecated for the cmor path — cmor yamls are now self-contained.
@@ -113,7 +114,7 @@ def get_combined_cmoryaml( yamlfile: Union[str, Path],
         #fre_logger.debug('... comb_cmor_updated_list = ...\n %s', pformat(comb_cmor_updated_list))
         ##assert False # good.
     except Exception as exc:
-        raise Exception(f"CmorYaml.combine_experiment failed for some reason.\n exc =\n {exc}") from exc
+        log_and_raise(f"CmorYaml.combine_experiment failed for some reason.\n exc =\n {exc}", Exception, exc=exc)
 
     try:
         fre_logger.info('\ncalling CmorYaml.merge_cmor_yaml(), for full_cmor_yaml.\n'
@@ -123,7 +124,7 @@ def get_combined_cmoryaml( yamlfile: Union[str, Path],
         #fre_logger.debug('... full_cmor_yaml = ...\n %s', pformat(full_cmor_yaml))
         ##assert False # good.
     except Exception as exc:
-        raise Exception(f"CmorYaml.merge_cmor_yaml failed for some reason.\n exc =\n {exc}") from exc
+        log_and_raise(f"CmorYaml.merge_cmor_yaml failed for some reason.\n exc =\n {exc}", Exception, exc=exc)
 
     cleaned_yaml = CmorYaml.clean_yaml(full_cmor_yaml)
     fre_logger.info("Combined cmor-yaml information cleaned+saved as dictionary")
@@ -211,6 +212,6 @@ def consolidate_yamls(yamlfile:str, experiment:str, platform:str,
 #        yml_dict = get_combined_cmoryaml( CmorYaml, output )
         fre_logger.info('... done attempting to combine cmor yaml info')
     else:
-        raise ValueError("'use' value is not valid; must be one of: 'compile', 'pp', or 'cmor'")
+        log_and_raise("'use' value is not valid; must be one of: 'compile', 'pp', or 'cmor'", ValueError)
 
     return yml_dict
diff --git a/fre/yamltools/helpers.py b/fre/yamltools/helpers.py
index 858458ec2..934f80705 100644
--- a/fre/yamltools/helpers.py
+++ b/fre/yamltools/helpers.py
@@ -14,6 +14,7 @@
 
 from . import *
 
+from fre import log_and_raise
 
 fre_logger = logging.getLogger(__name__)
 
@@ -81,7 +82,7 @@ def experiment_check(mainyaml_dir, experiment, loaded_yaml):
         exp_list.append(i.get("name"))
 
     if experiment not in exp_list:
-        raise NameError(f"{experiment} is not in the list of experiments")
+        log_and_raise(f"{experiment} is not in the list of experiments", NameError)
 
     # Extract yaml path for exp. provided
     # if experiment matches name in list of experiments in yaml, extract file path
@@ -95,12 +96,12 @@ def experiment_check(mainyaml_dir, experiment, loaded_yaml):
         analysisyaml=i.get("analysis")
 
         if expyaml is None:
-            raise ValueError("No experiment yaml path given!")
+            log_and_raise("No experiment yaml path given!", ValueError)
 
         for e in expyaml:
             ey = Path( os.path.join(mainyaml_dir, e) )
             if not ey.exists():
-                raise ValueError(f"Experiment yaml path given ({e}) does not exist.")
+                log_and_raise(f"Experiment yaml path given ({e}) does not exist.", ValueError)
             ey_path.append(ey)
 
         # Currently, if there are no analysis scripts defined, set None
@@ -111,7 +112,7 @@ def experiment_check(mainyaml_dir, experiment, loaded_yaml):
                 # prepend the directory containing the yaml
                 ay = Path(os.path.join(mainyaml_dir,a))
                 if not ay.exists():
-                    raise ValueError("Incorrect analysis yaml path given; does not exist.")
+                    log_and_raise("Incorrect analysis yaml path given; does not exist.", ValueError)
                 ay_path.append(ay)
 
         return (ey_path, ay_path)
@@ -166,6 +167,6 @@ def validate_yaml(yaml, schema_path):
         fre_logger.info("    YAML dictionary VALID.\n")
         return True
     except:
-        raise ValueError("    YAML dictionary NOT VALID.\n")
+        log_and_raise("    YAML dictionary NOT VALID.\n", ValueError)
     finally:
         fre_logger.setLevel(former_log_level)
diff --git a/fre/yamltools/info_parsers/analysis_info_parser.py b/fre/yamltools/info_parsers/analysis_info_parser.py
index ac24fe8db..ed6787a4d 100644
--- a/fre/yamltools/info_parsers/analysis_info_parser.py
+++ b/fre/yamltools/info_parsers/analysis_info_parser.py
@@ -3,6 +3,7 @@
 '''
 import os
 import logging
+from fre import log_and_raise
 #import pprint
 
 from fre.yamltools.helpers import experiment_check, clean_yaml
@@ -217,19 +218,19 @@ def combine(self):
         try:
             yaml_content_str = self.combine_model()
         except Exception as exc:
-            raise ValueError("ERR:  Could not merge model yaml config with name, platform, and target.") from exc
+            log_and_raise("ERR:  Could not merge model yaml config with name, platform, and target.", ValueError, exc=exc)
 
         # Merge settings into combined file
         try:
             yaml_content_str = self.combine_settings(yaml_content_str)
         except Exception as exc:
-            raise ValueError("ERR: Could not merge setting config with model config.") from exc
+            log_and_raise("ERR: Could not merge setting config with model config.", ValueError, exc=exc)
 
         # Merge analysis yamls, if defined, into combined file
         try:
             comb_analysis_updated_list = self.combine_yamls(yaml_content_str)
         except Exception as exc:
-            raise ValueError("ERR:  Could not merge analysis yaml config with model and setting config") from exc
+            log_and_raise("ERR:  Could not merge analysis yaml config with model and setting config", ValueError, exc=exc)
 
         # Merge model/analysis yamls if more than 1 is defined
         # (without overwriting the yaml)
@@ -237,11 +238,11 @@ def combine(self):
             full_combined = self.merge_multiple_yamls(comb_analysis_updated_list,
                                                       yaml_content_str)
         except Exception as exc:
-            raise ValueError("ERR: Could not merge multiple analysis yaml configs together.") from exc
+            log_and_raise("ERR: Could not merge multiple analysis yaml configs together.", ValueError, exc=exc)
 
         try:
             cleaned_yaml = clean_yaml(full_combined)
         except Exception as exc:
-            raise ValueError("The final YAML could not cleaned.") from exc
+            log_and_raise("The final YAML could not cleaned.", ValueError, exc=exc)
 
         return cleaned_yaml
diff --git a/fre/yamltools/info_parsers/cmor_info_parser.py b/fre/yamltools/info_parsers/cmor_info_parser.py
index 77fa77cbc..115e9f7f5 100644
--- a/fre/yamltools/info_parsers/cmor_info_parser.py
+++ b/fre/yamltools/info_parsers/cmor_info_parser.py
@@ -37,6 +37,7 @@
 import logging
 fre_logger = logging.getLogger(__name__)
 
+from fre import log_and_raise
 # this boots yaml with !join- see __init__
 from . import *
 
@@ -65,7 +66,7 @@ def experiment_check( mainyaml_dir: Union[str, Path],
         exp_list.append(i.get("name"))
 
     if experiment not in exp_list:
-        raise NameError(f"{experiment} is not in the list of experiments")
+        log_and_raise(f"{experiment} is not in the list of experiments", NameError)
 
     # Extract yaml path for exp. provided
     # if experiment matches name in list of experiments in yaml, extract file path
@@ -84,12 +85,12 @@ def experiment_check( mainyaml_dir: Union[str, Path],
         else:
             grid_yaml_path=os.path.join(mainyaml_dir, gridyaml)
             if not Path(grid_yaml_path).exists():
-                raise FileNotFoundError('%s not found!!!', grid_yaml_path)
+                log_and_raise(f'{grid_yaml_path} not found!!!', FileNotFoundError)
 
         ppyamls=i.get('pp')
         fre_logger.info(f'ppyamls is going to look like ppyamls=\n{ppyamls}')
         if ppyamls is None:
-            raise ValueError(f"no ppyaml paths found under experiment = {experiment}")
+            log_and_raise(f"no ppyaml paths found under experiment = {experiment}", ValueError)
 
         #ppsettingsyaml=None
         #for ppyaml in ppyamls:
@@ -111,17 +112,17 @@ def experiment_check( mainyaml_dir: Union[str, Path],
 
         cmoryaml=i.get("cmor")[0]
         if cmoryaml is None:
-            raise ValueError("No experiment yaml path given!")
+            log_and_raise("No experiment yaml path given!", ValueError)
 
         fre_logger.info(f'cmoryaml={cmoryaml} found- now checking for existence.')
         if not Path(os.path.join(mainyaml_dir, cmoryaml)).exists():
-            raise FileNotFoundError(f'cmoryaml={cmoryaml} does not exist!')
+            log_and_raise(f'cmoryaml={cmoryaml} does not exist!', FileNotFoundError)
 
         cmor_yaml_path = Path( os.path.join(mainyaml_dir, cmoryaml) )
         break
 
     if cmor_yaml_path is None:
-        raise ValueError('... something wrong... cmor_yaml_path is None... it should not be none!')
+        log_and_raise('... something wrong... cmor_yaml_path is None... it should not be none!', ValueError)
 
     fre_logger.info(f'cmor_info_parser\'s experiment_check about to return cmor_yaml_path!')
     return cmor_yaml_path, settings_yaml_path, grid_yaml_path
@@ -271,7 +272,7 @@ def combine_experiment( self,
 
         fre_logger.info(f'cmory_path = {cmory_path}')
         if cmory_path is None:
-            raise ValueError('cmory_path is none!')
+            log_and_raise('cmory_path is none!', ValueError)
 
         #fre_logger.info(f'ppsettingsy_path = {ppsettingsy_path}')
         #if ppsettingsy_path is None:
@@ -324,7 +325,7 @@ def merge_cmor_yaml( self,
         :rtype: dict
         """
         if cmor_list is None:
-            raise ValueError('cmor_list is none and should not be!!!')
+            log_and_raise('cmor_list is none and should not be!!!', ValueError)
         #fre_logger.debug("loaded_yaml =\n  %s", pformat(loaded_yaml))
         #fre_logger.debug("cmor_list =\n  %s", pformat(cmor_list))
         
diff --git a/fre/yamltools/info_parsers/compile_info_parser.py b/fre/yamltools/info_parsers/compile_info_parser.py
index 4cca5395d..a0ace58f9 100644
--- a/fre/yamltools/info_parsers/compile_info_parser.py
+++ b/fre/yamltools/info_parsers/compile_info_parser.py
@@ -3,6 +3,7 @@
 '''
 import os
 import logging
+from fre import log_and_raise
 # this boots yaml with !join- see __init__
 #from fre.yamltools import *
 from fre.yamltools.helpers import clean_yaml
@@ -31,7 +32,7 @@ def get_compile_paths(full_path, yaml_content):
     for key,value in yml.items():
         if key == "build":
             if (value.get("platformYaml") or value.get("compileYaml")) is None:
-                raise ValueError("Compile or platform yaml not defined")
+                log_and_raise("Compile or platform yaml not defined", ValueError)
 
             py_path = os.path.join(full_path,value.get("platformYaml"))
             cy_path = os.path.join(full_path,value.get("compileYaml"))
@@ -164,24 +165,24 @@ def combine(self):
         try:
             yaml_content=self.combine_model()
         except Exception as exc:
-            raise ValueError("ERR: Could not merge model yaml config with name, platform, and target.") from exc
+            log_and_raise("ERR: Could not merge model yaml config with name, platform, and target.", ValueError, exc=exc)
 
         # Merge compile into combined file to create updated yaml_content/yaml
         try:
             yaml_content = self.combine_compile(yaml_content)
         except Exception as exc:
-            raise ValueError("ERR: Could not merge compile yaml config with model config.") from exc
+            log_and_raise("ERR: Could not merge compile yaml config with model config.", ValueError, exc=exc)
 
         # Merge platforms.yaml into combined file
         try:
             full_combined = self.combine_platforms(yaml_content)
         except Exception as exc:
-            raise ValueError("ERR: Could not merge platform yaml config with model and compile configs.") from exc
+            log_and_raise("ERR: Could not merge platform yaml config with model and compile configs.", ValueError, exc=exc)
 
         # Clean the yaml
         try:
             cleaned_yaml = clean_yaml(full_combined)
         except Exception as exc:
-            raise ValueError("The final YAML could not cleaned.") from exc
+            log_and_raise("The final YAML could not cleaned.", ValueError, exc=exc)
 
         return cleaned_yaml
diff --git a/fre/yamltools/info_parsers/pp_info_parser.py b/fre/yamltools/info_parsers/pp_info_parser.py
index aeb228ecd..0075e8d63 100644
--- a/fre/yamltools/info_parsers/pp_info_parser.py
+++ b/fre/yamltools/info_parsers/pp_info_parser.py
@@ -5,6 +5,7 @@
 import logging
 import pprint
 
+from fre import log_and_raise
 from fre.yamltools.helpers import experiment_check, clean_yaml
 from fre.yamltools.abstract_classes import MergePPANYamls
 #from fre.yamltools.val_yml_structures import ModelYmlStructure
@@ -131,7 +132,7 @@ def combine_yamls(self, yaml_content_str: str):
         ## COMBINE EXPERIMENT YAML INFO
         # If only 1 pp yaml defined, combine with model yaml
         if ey_path is None:
-            raise ValueError('if ey_path is None, then pp_yamls will be an empty list. Exit!')
+            log_and_raise('if ey_path is None, then pp_yamls will be an empty list. Exit!', ValueError)
 
         elif len(ey_path) == 1:
             #expyaml_path = os.path.join(mainyaml_dir, i)
@@ -239,18 +240,18 @@ def combine(self):
             # Merge model into combined file
             yaml_content_str = self.combine_model()
         except Exception as exc:
-            raise ValueError("ERR: Could not merge model yaml config with name, platform, and target.") from exc
+            log_and_raise("ERR: Could not merge model yaml config with name, platform, and target.", ValueError, exc=exc)
         try:
             # Merge model into combined file
             yaml_content_str = self.combine_settings(yaml_content_str)
         except Exception as exc:
-            raise ValueError("ERR: Could not merge setting config with model config.") from exc
+            log_and_raise("ERR: Could not merge setting config with model config.", ValueError, exc=exc)
 
         try:
             # Merge pp yamls, if defined, into combined file
             comb_pp_updated_list = self.combine_yamls(yaml_content_str)
         except Exception as exc:
-            raise ValueError("ERR: Could not merge pp yaml config with model and setting config.") from exc
+            log_and_raise("ERR: Could not merge pp yaml config with model and setting config.", ValueError, exc=exc)
 
         try:
             # Merge model/pp yamls if more than 1 is defined
@@ -258,11 +259,11 @@ def combine(self):
             full_combined = self.merge_multiple_yamls(comb_pp_updated_list,
                                                       yaml_content_str)
         except Exception as exc:
-            raise ValueError("ERR: Could not merge multiple pp yaml configs together.") from exc
+            log_and_raise("ERR: Could not merge multiple pp yaml configs together.", ValueError, exc=exc)
 
         try:
             cleaned_yaml = clean_yaml(full_combined)
         except Exception as exc:
-            raise ValueError("The final YAML could not cleaned.") from exc
+            log_and_raise("The final YAML could not cleaned.", ValueError, exc=exc)
 
         return cleaned_yaml

From 5cf50b11df815db445aa2bf31a8f8d20782de42b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Apr 2026 19:42:34 +0000
Subject: [PATCH 07/10] Add -> NoReturn annotation to log_and_raise to fix
 pylint possibly-used-before-assignment errors

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/6e92661a-f061-4b23-a675-7ddeb69b0a21

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/fre/__init__.py b/fre/__init__.py
index 9b568a244..e24d08175 100644
--- a/fre/__init__.py
+++ b/fre/__init__.py
@@ -4,6 +4,7 @@
 
 import logging
 import os
+from typing import NoReturn
 version = os.getenv("GIT_DESCRIBE_TAG", "2026.01.alpha2")
 __version__ = version
 
@@ -16,7 +17,7 @@
                     encoding = 'utf-8' )
 
 
-def log_and_raise(msg, exc_type=ValueError, exc=None):
+def log_and_raise(msg, exc_type=ValueError, exc=None) -> NoReturn:
     """
     Log an error message via fre_logger and raise an exception with the same message.
     Avoids the need to duplicate error text in both fre_logger.error() and raise calls.

From 202b5b39a97c7fa8ac8da359944ea60398d56fef Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Mon, 6 Apr 2026 15:51:52 -0400
Subject: [PATCH 08/10] Improve error logging in log_and_raise function

Replace fre_logger.error with fre_logger.exception for better error logging.
---
 fre/__init__.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/fre/__init__.py b/fre/__init__.py
index e24d08175..edd85aca0 100644
--- a/fre/__init__.py
+++ b/fre/__init__.py
@@ -27,6 +27,9 @@ def log_and_raise(msg, exc_type=ValueError, exc=None) -> NoReturn:
     :param exc_type: Exception class to raise. Defaults to ValueError.
     :type exc_type: type
     :param exc: Optional original exception to chain from (uses ``raise ... from exc``).
+                When provided, logging uses ``fre_logger.exception()`` to capture the
+                traceback. Should be called from within an ``except`` block for full
+                traceback detail.
     :type exc: Exception, optional
     :raises exc_type: Always raised with the given message.
 
@@ -42,7 +45,8 @@ def log_and_raise(msg, exc_type=ValueError, exc=None) -> NoReturn:
         except KeyError as e:
             log_and_raise("update failed", KeyError, exc=e)
     """
-    fre_logger.error(msg, stacklevel=2)
     if exc is not None:
+        fre_logger.exception(msg, stacklevel=2)
         raise exc_type(msg) from exc
+    fre_logger.error(msg, stacklevel=2)
     raise exc_type(msg)

From 95c375dc1627d14f806b350830b3d55f1a9b9591 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 6 Apr 2026 20:07:14 +0000
Subject: [PATCH 09/10] Align log_and_raise with Python logging best practices;
 add log-file traceback tests

Per Python logging best practices (PEP 282, logging HOWTO):
- Use exc_info=True (not logger.exception) for caught exception tracebacks
- Use stack_info=True to always include call-site stack trace in log output
- Both ensure Traceback info reaches log files set up via fre -l

New tests verify that when a FileHandler is attached (simulating
fre -l ./logger_output.log):
- stack trace appears in log file for simple raises (stack_info=True)
- caught exception traceback appears in log file for chained raises
  (exc_info=True)

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/73b3875d-4130-4999-9488-0dc773ca1c45

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/__init__.py                     | 21 +++++--
 fre/tests/test_fre_log_and_raise.py | 89 +++++++++++++++++++++++++++++
 2 files changed, 105 insertions(+), 5 deletions(-)

diff --git a/fre/__init__.py b/fre/__init__.py
index edd85aca0..2c4784d7e 100644
--- a/fre/__init__.py
+++ b/fre/__init__.py
@@ -22,14 +22,25 @@ def log_and_raise(msg, exc_type=ValueError, exc=None) -> NoReturn:
     Log an error message via fre_logger and raise an exception with the same message.
     Avoids the need to duplicate error text in both fre_logger.error() and raise calls.
 
+    Per Python logging best practices (see :pep:`282` and the
+    `logging HOWTO <https://docs.python.org/3/howto/logging.html>`_):
+
+    * ``exc_info=True`` is passed when *exc* is given so the caught exception's
+      traceback is written to every configured handler (including any log file
+      set up via ``fre -l``).
+    * ``stack_info=True`` is always passed so the call-site stack trace appears
+      in every handler, making it easy to locate the origin of the error in a
+      log file.
+    * ``stacklevel=2`` attributes the log record to the **caller** of
+      ``log_and_raise``, not this helper itself.
+
     :param msg: Error message to log and include in the exception.
     :type msg: str
     :param exc_type: Exception class to raise. Defaults to ValueError.
     :type exc_type: type
     :param exc: Optional original exception to chain from (uses ``raise ... from exc``).
-                When provided, logging uses ``fre_logger.exception()`` to capture the
-                traceback. Should be called from within an ``except`` block for full
-                traceback detail.
+                When provided, ``exc_info=True`` is set so the caught exception's
+                traceback is included in the log output.
     :type exc: Exception, optional
     :raises exc_type: Always raised with the given message.
 
@@ -46,7 +57,7 @@ def log_and_raise(msg, exc_type=ValueError, exc=None) -> NoReturn:
             log_and_raise("update failed", KeyError, exc=e)
     """
     if exc is not None:
-        fre_logger.exception(msg, stacklevel=2)
+        fre_logger.error(msg, exc_info=True, stack_info=True, stacklevel=2)
         raise exc_type(msg) from exc
-    fre_logger.error(msg, stacklevel=2)
+    fre_logger.error(msg, stack_info=True, stacklevel=2)
     raise exc_type(msg)
diff --git a/fre/tests/test_fre_log_and_raise.py b/fre/tests/test_fre_log_and_raise.py
index a08728bc1..aaebadb62 100644
--- a/fre/tests/test_fre_log_and_raise.py
+++ b/fre/tests/test_fre_log_and_raise.py
@@ -7,9 +7,12 @@
 - supports exception chaining via the exc parameter
 - defaults to ValueError when no exc_type is given
 - reports the correct caller in log output (not log_and_raise itself)
+- writes stack trace info to a log file (simulating ``fre -l ./log.log``)
+- writes exception traceback to a log file when exc is provided
 """
 
 import logging
+from pathlib import Path
 
 import pytest
 
@@ -54,3 +57,89 @@ def test_log_and_raise_caller_in_log(caplog):
             break
     else:
         pytest.fail("expected log record not found")
+
+
+def test_log_and_raise_stack_trace_in_log_file(tmp_path):
+    """
+    Simulates ``fre -l ./logger_output.log`` by attaching a FileHandler to
+    the ``fre`` logger, then verifying that log_and_raise writes stack trace
+    information to the log file via ``stack_info=True``.
+
+    Per Python logging best practices (docs.python.org/3/howto/logging.html),
+    ``stack_info=True`` causes the current call stack to appear in the log
+    output, making it straightforward to locate the origin of an error.
+    """
+    from fre import FORMAT
+
+    log_file = tmp_path / "logger_output.log"
+
+    # Mirror fre.py: attach a FileHandler to the root 'fre' logger
+    base_logger = logging.getLogger("fre")
+    handler = logging.FileHandler(str(log_file), mode="w", encoding="utf-8")
+    handler.setFormatter(logging.Formatter(fmt=FORMAT))
+    handler.setLevel(logging.ERROR)
+    base_logger.addHandler(handler)
+
+    try:
+        with pytest.raises(ValueError, match="stack trace test"):
+            log_and_raise("stack trace test")
+    finally:
+        base_logger.removeHandler(handler)
+        handler.close()
+
+    log_content = log_file.read_text(encoding="utf-8")
+
+    # The error message itself must appear
+    assert "stack trace test" in log_content
+
+    # stack_info=True produces a "Stack (most recent call last):" block
+    assert "Stack (most recent call last):" in log_content
+
+    # The call stack should reference THIS test function
+    assert "test_log_and_raise_stack_trace_in_log_file" in log_content
+
+
+def test_log_and_raise_traceback_in_log_file(tmp_path):
+    """
+    Simulates ``fre -l ./logger_output.log`` and verifies that when
+    log_and_raise is called with ``exc`` (inside an except block), the
+    caught exception's traceback appears in the log file via
+    ``exc_info=True``.
+
+    This matches the Python best practice of using ``exc_info=True`` to
+    record the full traceback of a caught exception
+    (see docs.python.org/3/library/logging.html#logging.Logger.error).
+    """
+    from fre import FORMAT
+
+    log_file = tmp_path / "logger_output.log"
+
+    base_logger = logging.getLogger("fre")
+    handler = logging.FileHandler(str(log_file), mode="w", encoding="utf-8")
+    handler.setFormatter(logging.Formatter(fmt=FORMAT))
+    handler.setLevel(logging.ERROR)
+    base_logger.addHandler(handler)
+
+    try:
+        try:
+            raise RuntimeError("original failure")
+        except RuntimeError as caught:
+            with pytest.raises(OSError, match="wrapped failure"):
+                log_and_raise("wrapped failure", OSError, exc=caught)
+    finally:
+        base_logger.removeHandler(handler)
+        handler.close()
+
+    log_content = log_file.read_text(encoding="utf-8")
+
+    # The error message itself must appear
+    assert "wrapped failure" in log_content
+
+    # exc_info=True produces a "Traceback (most recent call last):" block
+    assert "Traceback (most recent call last):" in log_content
+
+    # The original exception type and message must appear in the traceback
+    assert "RuntimeError: original failure" in log_content
+
+    # stack_info=True also adds the call stack
+    assert "Stack (most recent call last):" in log_content

From 3b994053ce870f0ee1b62212f6df6902f1f29405 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 6 Apr 2026 20:08:18 +0000
Subject: [PATCH 10/10] Remove unused Path import from
 test_fre_log_and_raise.py

Agent-Logs-Url: https://github.com/NOAA-GFDL/fre-cli/sessions/73b3875d-4130-4999-9488-0dc773ca1c45

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
---
 fre/tests/test_fre_log_and_raise.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/fre/tests/test_fre_log_and_raise.py b/fre/tests/test_fre_log_and_raise.py
index aaebadb62..2cc907644 100644
--- a/fre/tests/test_fre_log_and_raise.py
+++ b/fre/tests/test_fre_log_and_raise.py
@@ -12,7 +12,6 @@
 """
 
 import logging
-from pathlib import Path
 
 import pytest